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1 ImportedSubstrateList<- read.csv("input1", stringsAsFactors=FALSE,header = FALSE)
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2 NegativeSubstrateList<- read.csv("input2", stringsAsFactors=FALSE)
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3 SubstrateBackgroundFrequency<- read.csv("input3", stringsAsFactors=FALSE, header = FALSE)
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4
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5 ScreenerFilename<-"screenerST.csv"
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6
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7
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8
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9 FILENAME<-"output1"
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10 FILENAME2<-"output2"
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11 FILENAME3<-"output3"
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12 FILENAME4<-"output4"
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13 FILENAME5<-"output5"
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14
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15
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16 SubstrateBackgroundFrequency<-t(SubstrateBackgroundFrequency)
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17 # number<-nrow(SubstrateBackgroundFrequency)-1
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18 SubstrateBackgroundFrequency<-SubstrateBackgroundFrequency[2:nrow(SubstrateBackgroundFrequency),]
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19 Sub<-na.omit(SubstrateBackgroundFrequency)
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20 SubstrateBackgroundFrequency<-Sub
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21
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22 args = commandArgs(trailingOnly=TRUE)
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23 TodaysKinase<-"AKT"
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24
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25 #as.character(args[1])
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26
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27
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28
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29
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30
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31
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32 OutputMatrix<-"KinaseMatrix.csv"
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33 CharacterizationTable<-"CharacterizationTableForThisKinase.csv"
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34 SDtable<-"SDtableforthisKinase"
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35 SiteSelectivityTable<-"SiteSelectivityForThisKinase"
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36
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37
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38
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39 substrates<-matrix(rep("A",times=((nrow(ImportedSubstrateList)-1)*15)),ncol = 15)
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40 #SeqsToBeScored<-"asdasd"
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41
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42 for (i in 2:nrow(ImportedSubstrateList))
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43 {
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44 substratemotif<-ImportedSubstrateList[i,4:18]
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45 T_or_S<-unlist(strsplit(as.character(substratemotif[8]),split = ""))
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46 substratemotif[8]<-T_or_S[2]
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47 #substratemotif<-paste(substratemotif,sep = "",collapse = "")
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48 j=i-1
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49 substratemotif<-unlist(substratemotif)
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50 substrates[j,1:15]<-substratemotif
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51 }
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52
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53 # SpacesToOs<-c(""="O",)
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54 # substrates<-SpacesToOs[substrates]
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55
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56 #SubstrateBackgroundFrequency[nrow(SubstrateBackgroundFrequency),2]
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57
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58 if(2==2){
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59 Amean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),2]), na.rm=TRUE)
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60 Cmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),3]), na.rm=TRUE)
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61 Dmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),4]), na.rm=TRUE)
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62 Emean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),5]), na.rm=TRUE)
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63 Fmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),6]), na.rm=TRUE)
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64 Gmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),7]), na.rm=TRUE)
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65 Hmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),8]), na.rm=TRUE)
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66 Imean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),9]), na.rm=TRUE)
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67 Kmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),10]), na.rm=TRUE)
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68 Lmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),11]), na.rm=TRUE)
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69 Mmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),12]), na.rm=TRUE)
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70 Nmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),13]), na.rm=TRUE)
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71 Pmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),14]), na.rm=TRUE)
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72 Qmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),15]), na.rm=TRUE)
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73 Rmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),16]), na.rm=TRUE)
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74 Smean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),17]), na.rm=TRUE)
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75 Tmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),18]), na.rm=TRUE)
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76 Vmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),19]), na.rm=TRUE)
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77 Wmean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),20]), na.rm=TRUE)
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78 Ymean<-mean(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),21]), na.rm=TRUE)
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79
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80 AllMeans<-c(Amean,Cmean,Dmean,Emean,Fmean,Gmean,Hmean,Imean,Kmean,Lmean,Mmean,Nmean,Pmean,Qmean,Rmean,Smean,Tmean,Vmean,Wmean,Ymean)
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81
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82 Asd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),2]), na.rm=TRUE)
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83 Csd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),3]), na.rm=TRUE)
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84 Dsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),4]), na.rm=TRUE)
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85 Esd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),5]), na.rm=TRUE)
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86 Fsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),6]), na.rm=TRUE)
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87 Gsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),7]), na.rm=TRUE)
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88 Hsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),8]), na.rm=TRUE)
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89 Isd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),9]), na.rm=TRUE)
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90 Ksd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),10]), na.rm=TRUE)
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91 Lsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),11]), na.rm=TRUE)
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92 Msd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),12]), na.rm=TRUE)
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93 Nsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),13]), na.rm=TRUE)
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94 Psd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),14]), na.rm=TRUE)
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95 Qsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),15]), na.rm=TRUE)
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96 Rsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),16]), na.rm=TRUE)
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97 Ssd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),17]), na.rm=TRUE)
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98 Tsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),18]), na.rm=TRUE)
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99 Vsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),19]), na.rm=TRUE)
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100 Wsd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),20]), na.rm=TRUE)
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101 Ysd<-sd(as.numeric(SubstrateBackgroundFrequency[1:(nrow(SubstrateBackgroundFrequency)),21]), na.rm=TRUE)
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102 }
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103 AllSDs<-c(Asd,Csd,Dsd,Esd,Fsd,Gsd,Hsd,Isd,Ksd,Lsd,Msd,Nsd,Psd,Qsd,Rsd,Ssd,Tsd,Vsd,Wsd,Ysd)
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104 #this is subbackfreq SDs
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105
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106 SBF_statisticalvalues<-cbind(AllMeans,AllSDs)
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107
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108 #create the percent table
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109 if (1==1){
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110 Column1<-substrates[,1]
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111 Column2<-substrates[,2]
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112 Column3<-substrates[,3]
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113 Column4<-substrates[,4]
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114 Column5<-substrates[,5]
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115 Column6<-substrates[,6]
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116 Column7<-substrates[,7]
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117 Column8<-substrates[,8]
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118 Column9<-substrates[,9]
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119 Column10<-substrates[,10]
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120 Column11<-substrates[,11]
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121 Column12<-substrates[,12]
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122 Column13<-substrates[,13]
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123 Column14<-substrates[,14]
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124 Column15<-substrates[,15]
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125
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126 spaces1<-sum((Column1%in% ""))
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127 spaces2<-sum(Column2%in% "")
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128 spaces3<-sum(Column3%in% "")
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129 spaces4<-sum(Column4%in% "")
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130 spaces5<-sum(Column5%in% "")
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131 spaces6<-sum(Column6%in% "")
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132 spaces7<-sum(Column7%in% "")
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133 spaces8<-sum(Column8%in% "")
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134 spaces9<-sum(Column9%in% "")
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135 spaces10<-sum(Column10%in% "")
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136 spaces11<-sum(Column11%in% "")
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137 spaces12<-sum(Column12%in% "")
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138 spaces13<-sum(Column13%in% "")
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139 spaces14<-sum(Column14%in% "")
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140 spaces15<-sum(Column15%in% "")
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141
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142 A1<-sum(Column1 %in% "A")/(length(Column1)-spaces1)
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143 A2<-sum(Column2 %in% "A")/(length(Column2)-spaces2)
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144 A3<-sum(Column3 %in% "A")/(length(Column3)-spaces3)
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145 A4<-sum(Column4 %in% "A")/(length(Column4)-spaces4)
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146 A5<-sum(Column5 %in% "A")/(length(Column5)-spaces5)
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147 A6<-sum(Column6 %in% "A")/(length(Column6)-spaces6)
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148 A7<-sum(Column7 %in% "A")/(length(Column7)-spaces7)
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149 A8<-sum(Column8 %in% "A")/(length(Column8)-spaces8)
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150 A9<-sum(Column9 %in% "A")/(length(Column9)-spaces9)
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151 A10<-sum(Column10 %in% "A")/(length(Column10)-spaces10)
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152 A11<-sum(Column11 %in% "A")/(length(Column11)-spaces11)
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153 A12<-sum(Column12 %in% "A")/(length(Column12)-spaces12)
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154 A13<-sum(Column13 %in% "A")/(length(Column13)-spaces13)
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155 A14<-sum(Column14 %in% "A")/(length(Column14)-spaces14)
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156 A15<-sum(Column15 %in% "A")/(length(Column15)-spaces15)
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157 AllAs<-cbind(A1,A2,A3,A4,A5,A6,A7,A8,A9,A10,A11,A12,A13,A14,A15)
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158
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159 C1<-sum(Column1 %in% "C")/(length(Column1)-spaces1)
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160 C2<-sum(Column2 %in% "C")/(length(Column2)-spaces2)
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161 C3<-sum(Column3 %in% "C")/(length(Column3)-spaces3)
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162 C4<-sum(Column4 %in% "C")/(length(Column4)-spaces4)
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163 C5<-sum(Column5 %in% "C")/(length(Column5)-spaces5)
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164 C6<-sum(Column6 %in% "C")/(length(Column6)-spaces6)
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165 C7<-sum(Column7 %in% "C")/(length(Column7)-spaces7)
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166 C8<-sum(Column8 %in% "C")/(length(Column8)-spaces8)
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167 C9<-sum(Column9 %in% "C")/(length(Column9)-spaces9)
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168 C10<-sum(Column10 %in% "C")/(length(Column10)-spaces10)
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169 C11<-sum(Column11 %in% "C")/(length(Column11)-spaces11)
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170 C12<-sum(Column12 %in% "C")/(length(Column12)-spaces12)
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171 C13<-sum(Column13 %in% "C")/(length(Column13)-spaces13)
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172 C14<-sum(Column14 %in% "C")/(length(Column14)-spaces14)
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173 C15<-sum(Column15 %in% "C")/(length(Column15)-spaces15)
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174 CllCs<-cbind(C1,C2,C3,C4,C5,C6,C7,C8,C9,C10,C11,C12,C13,C14,C15)
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175
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176 D1<-sum(Column1 %in% "D")/(length(Column1)-spaces1)
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177 D2<-sum(Column2 %in% "D")/(length(Column2)-spaces2)
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178 D3<-sum(Column3 %in% "D")/(length(Column3)-spaces3)
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179 D4<-sum(Column4 %in% "D")/(length(Column4)-spaces4)
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180 D5<-sum(Column5 %in% "D")/(length(Column5)-spaces5)
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181 D6<-sum(Column6 %in% "D")/(length(Column6)-spaces6)
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182 D7<-sum(Column7 %in% "D")/(length(Column7)-spaces7)
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183 D8<-sum(Column8 %in% "D")/(length(Column8)-spaces8)
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184 D9<-sum(Column9 %in% "D")/(length(Column9)-spaces9)
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185 D10<-sum(Column10 %in% "D")/(length(Column10)-spaces10)
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186 D11<-sum(Column11 %in% "D")/(length(Column11)-spaces11)
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187 D12<-sum(Column12 %in% "D")/(length(Column12)-spaces12)
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188 D13<-sum(Column13 %in% "D")/(length(Column13)-spaces13)
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189 D14<-sum(Column14 %in% "D")/(length(Column14)-spaces14)
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190 D15<-sum(Column15 %in% "D")/(length(Column15)-spaces15)
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191 DllDs<-cbind(D1,D2,D3,D4,D5,D6,D7,D8,D9,D10,D11,D12,D13,D14,D15)
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192
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193 E1<-sum(Column1 %in% "E")/(length(Column1)-spaces1)
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194 E2<-sum(Column2 %in% "E")/(length(Column2)-spaces2)
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195 E3<-sum(Column3 %in% "E")/(length(Column3)-spaces3)
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196 E4<-sum(Column4 %in% "E")/(length(Column4)-spaces4)
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197 E5<-sum(Column5 %in% "E")/(length(Column5)-spaces5)
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198 E6<-sum(Column6 %in% "E")/(length(Column6)-spaces6)
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199 E7<-sum(Column7 %in% "E")/(length(Column7)-spaces7)
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200 E8<-sum(Column8 %in% "E")/(length(Column8)-spaces8)
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201 E9<-sum(Column9 %in% "E")/(length(Column9)-spaces9)
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202 E10<-sum(Column10 %in% "E")/(length(Column10)-spaces10)
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203 E11<-sum(Column11 %in% "E")/(length(Column11)-spaces11)
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204 E12<-sum(Column12 %in% "E")/(length(Column12)-spaces12)
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205 E13<-sum(Column13 %in% "E")/(length(Column13)-spaces13)
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206 E14<-sum(Column14 %in% "E")/(length(Column14)-spaces14)
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207 E15<-sum(Column15 %in% "E")/(length(Column15)-spaces15)
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208 EllEs<-cbind(E1,E2,E3,E4,E5,E6,E7,E8,E9,E10,E11,E12,E13,E14,E15)
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209
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210
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211 F1<-sum(Column1 %in% "F")/(length(Column1)-spaces1)
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212 F2<-sum(Column2 %in% "F")/(length(Column2)-spaces2)
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213 F3<-sum(Column3 %in% "F")/(length(Column3)-spaces3)
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214 F4<-sum(Column4 %in% "F")/(length(Column4)-spaces4)
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215 F5<-sum(Column5 %in% "F")/(length(Column5)-spaces5)
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216 F6<-sum(Column6 %in% "F")/(length(Column6)-spaces6)
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217 F7<-sum(Column7 %in% "F")/(length(Column7)-spaces7)
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218 F8<-sum(Column8 %in% "F")/(length(Column8)-spaces8)
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219 F9<-sum(Column9 %in% "F")/(length(Column9)-spaces9)
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220 F10<-sum(Column10 %in% "F")/(length(Column10)-spaces10)
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221 F11<-sum(Column11 %in% "F")/(length(Column11)-spaces11)
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222 F12<-sum(Column12 %in% "F")/(length(Column12)-spaces12)
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223 F13<-sum(Column13 %in% "F")/(length(Column13)-spaces13)
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224 F14<-sum(Column14 %in% "F")/(length(Column14)-spaces14)
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225 F15<-sum(Column15 %in% "F")/(length(Column15)-spaces15)
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226 FllFs<-cbind(F1,F2,F3,F4,F5,F6,F7,F8,F9,F10,F11,F12,F13,F14,F15)
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227
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228
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229 G1<-sum(Column1 %in% "G")/(length(Column1)-spaces1)
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230 G2<-sum(Column2 %in% "G")/(length(Column2)-spaces2)
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231 G3<-sum(Column3 %in% "G")/(length(Column3)-spaces3)
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232 G4<-sum(Column4 %in% "G")/(length(Column4)-spaces4)
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233 G5<-sum(Column5 %in% "G")/(length(Column5)-spaces5)
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234 G6<-sum(Column6 %in% "G")/(length(Column6)-spaces6)
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235 G7<-sum(Column7 %in% "G")/(length(Column7)-spaces7)
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236 G8<-sum(Column8 %in% "G")/(length(Column8)-spaces8)
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237 G9<-sum(Column9 %in% "G")/(length(Column9)-spaces9)
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238 G10<-sum(Column10 %in% "G")/(length(Column10)-spaces10)
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239 G11<-sum(Column11 %in% "G")/(length(Column11)-spaces11)
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240 G12<-sum(Column12 %in% "G")/(length(Column12)-spaces12)
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241 G13<-sum(Column13 %in% "G")/(length(Column13)-spaces13)
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242 G14<-sum(Column14 %in% "G")/(length(Column14)-spaces14)
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243 G15<-sum(Column15 %in% "G")/(length(Column15)-spaces15)
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244 GllGs<-cbind(G1,G2,G3,G4,G5,G6,G7,G8,G9,G10,G11,G12,G13,G14,G15)
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245
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246
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247 H1<-sum(Column1 %in% "H")/(length(Column1)-spaces1)
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248 H2<-sum(Column2 %in% "H")/(length(Column2)-spaces2)
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249 H3<-sum(Column3 %in% "H")/(length(Column3)-spaces3)
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250 H4<-sum(Column4 %in% "H")/(length(Column4)-spaces4)
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251 H5<-sum(Column5 %in% "H")/(length(Column5)-spaces5)
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252 H6<-sum(Column6 %in% "H")/(length(Column6)-spaces6)
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253 H7<-sum(Column7 %in% "H")/(length(Column7)-spaces7)
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254 H8<-sum(Column8 %in% "H")/(length(Column8)-spaces8)
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255 H9<-sum(Column9 %in% "H")/(length(Column9)-spaces9)
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256 H10<-sum(Column10 %in% "H")/(length(Column10)-spaces10)
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257 H11<-sum(Column11 %in% "H")/(length(Column11)-spaces11)
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258 H12<-sum(Column12 %in% "H")/(length(Column12)-spaces12)
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259 H13<-sum(Column13 %in% "H")/(length(Column13)-spaces13)
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260 H14<-sum(Column14 %in% "H")/(length(Column14)-spaces14)
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261 H15<-sum(Column15 %in% "H")/(length(Column15)-spaces15)
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262 HllHs<-cbind(H1,H2,H3,H4,H5,H6,H7,H8,H9,H10,H11,H12,H13,H14,H15)
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263
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264
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265 I1<-sum(Column1 %in% "I")/(length(Column1)-spaces1)
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266 I2<-sum(Column2 %in% "I")/(length(Column2)-spaces2)
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267 I3<-sum(Column3 %in% "I")/(length(Column3)-spaces3)
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268 I4<-sum(Column4 %in% "I")/(length(Column4)-spaces4)
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269 I5<-sum(Column5 %in% "I")/(length(Column5)-spaces5)
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270 I6<-sum(Column6 %in% "I")/(length(Column6)-spaces6)
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271 I7<-sum(Column7 %in% "I")/(length(Column7)-spaces7)
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272 I8<-sum(Column8 %in% "I")/(length(Column8)-spaces8)
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273 I9<-sum(Column9 %in% "I")/(length(Column9)-spaces9)
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274 I10<-sum(Column10 %in% "I")/(length(Column10)-spaces10)
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275 I11<-sum(Column11 %in% "I")/(length(Column11)-spaces11)
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276 I12<-sum(Column12 %in% "I")/(length(Column12)-spaces12)
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277 I13<-sum(Column13 %in% "I")/(length(Column13)-spaces13)
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278 I14<-sum(Column14 %in% "I")/(length(Column14)-spaces14)
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279 I15<-sum(Column15 %in% "I")/(length(Column15)-spaces15)
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280 IllIs<-cbind(I1,I2,I3,I4,I5,I6,I7,I8,I9,I10,I11,I12,I13,I14,I15)
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281
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282
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283 K1<-sum(Column1 %in% "K")/(length(Column1)-spaces1)
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284 K2<-sum(Column2 %in% "K")/(length(Column2)-spaces2)
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285 K3<-sum(Column3 %in% "K")/(length(Column3)-spaces3)
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286 K4<-sum(Column4 %in% "K")/(length(Column4)-spaces4)
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287 K5<-sum(Column5 %in% "K")/(length(Column5)-spaces5)
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288 K6<-sum(Column6 %in% "K")/(length(Column6)-spaces6)
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289 K7<-sum(Column7 %in% "K")/(length(Column7)-spaces7)
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290 K8<-sum(Column8 %in% "K")/(length(Column8)-spaces8)
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291 K9<-sum(Column9 %in% "K")/(length(Column9)-spaces9)
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292 K10<-sum(Column10 %in% "K")/(length(Column10)-spaces10)
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293 K11<-sum(Column11 %in% "K")/(length(Column11)-spaces11)
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294 K12<-sum(Column12 %in% "K")/(length(Column12)-spaces12)
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295 K13<-sum(Column13 %in% "K")/(length(Column13)-spaces13)
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296 K14<-sum(Column14 %in% "K")/(length(Column14)-spaces14)
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297 K15<-sum(Column15 %in% "K")/(length(Column15)-spaces15)
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298 KllKs<-cbind(K1,K2,K3,K4,K5,K6,K7,K8,K9,K10,K11,K12,K13,K14,K15)
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299
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300
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301 L1<-sum(Column1 %in% "L")/(length(Column1)-spaces1)
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302 L2<-sum(Column2 %in% "L")/(length(Column2)-spaces2)
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303 L3<-sum(Column3 %in% "L")/(length(Column3)-spaces3)
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304 L4<-sum(Column4 %in% "L")/(length(Column4)-spaces4)
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305 L5<-sum(Column5 %in% "L")/(length(Column5)-spaces5)
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306 L6<-sum(Column6 %in% "L")/(length(Column6)-spaces6)
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307 L7<-sum(Column7 %in% "L")/(length(Column7)-spaces7)
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308 L8<-sum(Column8 %in% "L")/(length(Column8)-spaces8)
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309 L9<-sum(Column9 %in% "L")/(length(Column9)-spaces9)
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310 L10<-sum(Column10 %in% "L")/(length(Column10)-spaces10)
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311 L11<-sum(Column11 %in% "L")/(length(Column11)-spaces11)
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312 L12<-sum(Column12 %in% "L")/(length(Column12)-spaces12)
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313 L13<-sum(Column13 %in% "L")/(length(Column13)-spaces13)
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314 L14<-sum(Column14 %in% "L")/(length(Column14)-spaces14)
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315 L15<-sum(Column15 %in% "L")/(length(Column15)-spaces15)
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316 LllLs<-cbind(L1,L2,L3,L4,L5,L6,L7,L8,L9,L10,L11,L12,L13,L14,L15)
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317
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318
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319 M1<-sum(Column1 %in% "M")/(length(Column1)-spaces1)
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320 M2<-sum(Column2 %in% "M")/(length(Column2)-spaces2)
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321 M3<-sum(Column3 %in% "M")/(length(Column3)-spaces3)
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322 M4<-sum(Column4 %in% "M")/(length(Column4)-spaces4)
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323 M5<-sum(Column5 %in% "M")/(length(Column5)-spaces5)
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324 M6<-sum(Column6 %in% "M")/(length(Column6)-spaces6)
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325 M7<-sum(Column7 %in% "M")/(length(Column7)-spaces7)
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326 M8<-sum(Column8 %in% "M")/(length(Column8)-spaces8)
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327 M9<-sum(Column9 %in% "M")/(length(Column9)-spaces9)
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328 M10<-sum(Column10 %in% "M")/(length(Column10)-spaces10)
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329 M11<-sum(Column11 %in% "M")/(length(Column11)-spaces11)
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330 M12<-sum(Column12 %in% "M")/(length(Column12)-spaces12)
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331 M13<-sum(Column13 %in% "M")/(length(Column13)-spaces13)
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332 M14<-sum(Column14 %in% "M")/(length(Column14)-spaces14)
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333 M15<-sum(Column15 %in% "M")/(length(Column15)-spaces15)
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334 MllMs<-cbind(M1,M2,M3,M4,M5,M6,M7,M8,M9,M10,M11,M12,M13,M14,M15)
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335
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336
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337 N1<-sum(Column1 %in% "N")/(length(Column1)-spaces1)
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338 N2<-sum(Column2 %in% "N")/(length(Column2)-spaces2)
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339 N3<-sum(Column3 %in% "N")/(length(Column3)-spaces3)
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340 N4<-sum(Column4 %in% "N")/(length(Column4)-spaces4)
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341 N5<-sum(Column5 %in% "N")/(length(Column5)-spaces5)
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342 N6<-sum(Column6 %in% "N")/(length(Column6)-spaces6)
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343 N7<-sum(Column7 %in% "N")/(length(Column7)-spaces7)
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344 N8<-sum(Column8 %in% "N")/(length(Column8)-spaces8)
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345 N9<-sum(Column9 %in% "N")/(length(Column9)-spaces9)
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346 N10<-sum(Column10 %in% "N")/(length(Column10)-spaces10)
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347 N11<-sum(Column11 %in% "N")/(length(Column11)-spaces11)
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348 N12<-sum(Column12 %in% "N")/(length(Column12)-spaces12)
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349 N13<-sum(Column13 %in% "N")/(length(Column13)-spaces13)
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350 N14<-sum(Column14 %in% "N")/(length(Column14)-spaces14)
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351 N15<-sum(Column15 %in% "N")/(length(Column15)-spaces15)
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352 NllNs<-cbind(N1,N2,N3,N4,N5,N6,N7,N8,N9,N10,N11,N12,N13,N14,N15)
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353
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354
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355 P1<-sum(Column1 %in% "P")/(length(Column1)-spaces1)
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356 P2<-sum(Column2 %in% "P")/(length(Column2)-spaces2)
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357 P3<-sum(Column3 %in% "P")/(length(Column3)-spaces3)
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358 P4<-sum(Column4 %in% "P")/(length(Column4)-spaces4)
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359 P5<-sum(Column5 %in% "P")/(length(Column5)-spaces5)
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360 P6<-sum(Column6 %in% "P")/(length(Column6)-spaces6)
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361 P7<-sum(Column7 %in% "P")/(length(Column7)-spaces7)
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362 P8<-sum(Column8 %in% "P")/(length(Column8)-spaces8)
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363 P9<-sum(Column9 %in% "P")/(length(Column9)-spaces9)
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364 P10<-sum(Column10 %in% "P")/(length(Column10)-spaces10)
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365 P11<-sum(Column11 %in% "P")/(length(Column11)-spaces11)
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366 P12<-sum(Column12 %in% "P")/(length(Column12)-spaces12)
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367 P13<-sum(Column13 %in% "P")/(length(Column13)-spaces13)
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368 P14<-sum(Column14 %in% "P")/(length(Column14)-spaces14)
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369 P15<-sum(Column15 %in% "P")/(length(Column15)-spaces15)
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370 PllPs<-cbind(P1,P2,P3,P4,P5,P6,P7,P8,P9,P10,P11,P12,P13,P14,P15)
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371
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372
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373 Q1<-sum(Column1 %in% "Q")/(length(Column1)-spaces1)
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374 Q2<-sum(Column2 %in% "Q")/(length(Column2)-spaces2)
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375 Q3<-sum(Column3 %in% "Q")/(length(Column3)-spaces3)
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376 Q4<-sum(Column4 %in% "Q")/(length(Column4)-spaces4)
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377 Q5<-sum(Column5 %in% "Q")/(length(Column5)-spaces5)
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378 Q6<-sum(Column6 %in% "Q")/(length(Column6)-spaces6)
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379 Q7<-sum(Column7 %in% "Q")/(length(Column7)-spaces7)
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380 Q8<-sum(Column8 %in% "Q")/(length(Column8)-spaces8)
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381 Q9<-sum(Column9 %in% "Q")/(length(Column9)-spaces9)
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382 Q10<-sum(Column10 %in% "Q")/(length(Column10)-spaces10)
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383 Q11<-sum(Column11 %in% "Q")/(length(Column11)-spaces11)
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384 Q12<-sum(Column12 %in% "Q")/(length(Column12)-spaces12)
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385 Q13<-sum(Column13 %in% "Q")/(length(Column13)-spaces13)
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386 Q14<-sum(Column14 %in% "Q")/(length(Column14)-spaces14)
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387 Q15<-sum(Column15 %in% "Q")/(length(Column15)-spaces15)
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388 QllQs<-cbind(Q1,Q2,Q3,Q4,Q5,Q6,Q7,Q8,Q9,Q10,Q11,Q12,Q13,Q14,Q15)
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389
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390
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391 R1<-sum(Column1 %in% "R")/(length(Column1)-spaces1)
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392 R2<-sum(Column2 %in% "R")/(length(Column2)-spaces2)
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393 R3<-sum(Column3 %in% "R")/(length(Column3)-spaces3)
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394 R4<-sum(Column4 %in% "R")/(length(Column4)-spaces4)
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395 R5<-sum(Column5 %in% "R")/(length(Column5)-spaces5)
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396 R6<-sum(Column6 %in% "R")/(length(Column6)-spaces6)
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397 R7<-sum(Column7 %in% "R")/(length(Column7)-spaces7)
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398 R8<-sum(Column8 %in% "R")/(length(Column8)-spaces8)
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399 R9<-sum(Column9 %in% "R")/(length(Column9)-spaces9)
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400 R10<-sum(Column10 %in% "R")/(length(Column10)-spaces10)
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401 R11<-sum(Column11 %in% "R")/(length(Column11)-spaces11)
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402 R12<-sum(Column12 %in% "R")/(length(Column12)-spaces12)
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403 R13<-sum(Column13 %in% "R")/(length(Column13)-spaces13)
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404 R14<-sum(Column14 %in% "R")/(length(Column14)-spaces14)
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405 R15<-sum(Column15 %in% "R")/(length(Column15)-spaces15)
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406 RllRs<-cbind(R1,R2,R3,R4,R5,R6,R7,R8,R9,R10,R11,R12,R13,R14,R15)
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|
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407
|
|
|
408
|
|
|
409 S1<-sum(Column1 %in% "S")/(length(Column1)-spaces1)
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410 S2<-sum(Column2 %in% "S")/(length(Column2)-spaces2)
|
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411 S3<-sum(Column3 %in% "S")/(length(Column3)-spaces3)
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412 S4<-sum(Column4 %in% "S")/(length(Column4)-spaces4)
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413 S5<-sum(Column5 %in% "S")/(length(Column5)-spaces5)
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414 S6<-sum(Column6 %in% "S")/(length(Column6)-spaces6)
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415 S7<-sum(Column7 %in% "S")/(length(Column7)-spaces7)
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416 S8<-sum(Column8 %in% "S")/(length(Column8)-spaces8)
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417 S9<-sum(Column9 %in% "S")/(length(Column9)-spaces9)
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418 S10<-sum(Column10 %in% "S")/(length(Column10)-spaces10)
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419 S11<-sum(Column11 %in% "S")/(length(Column11)-spaces11)
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420 S12<-sum(Column12 %in% "S")/(length(Column12)-spaces12)
|
|
|
421 S13<-sum(Column13 %in% "S")/(length(Column13)-spaces13)
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|
|
422 S14<-sum(Column14 %in% "S")/(length(Column14)-spaces14)
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423 S15<-sum(Column15 %in% "S")/(length(Column15)-spaces15)
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|
424 SllSs<-cbind(S1,S2,S3,S4,S5,S6,S7,S8,S9,S10,S11,S12,S13,S14,S15)
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|
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425
|
|
|
426
|
|
|
427 T1<-sum(Column1 %in% "T")/(length(Column1)-spaces1)
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|
|
428 T2<-sum(Column2 %in% "T")/(length(Column2)-spaces2)
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|
|
429 T3<-sum(Column3 %in% "T")/(length(Column3)-spaces3)
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|
|
430 T4<-sum(Column4 %in% "T")/(length(Column4)-spaces4)
|
|
|
431 T5<-sum(Column5 %in% "T")/(length(Column5)-spaces5)
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|
|
432 T6<-sum(Column6 %in% "T")/(length(Column6)-spaces6)
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|
|
433 T7<-sum(Column7 %in% "T")/(length(Column7)-spaces7)
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|
|
434 T8<-sum(Column8 %in% "T")/(length(Column8)-spaces8)
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|
|
435 T9<-sum(Column9 %in% "T")/(length(Column9)-spaces9)
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|
436 T10<-sum(Column10 %in% "T")/(length(Column10)-spaces10)
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|
|
437 T11<-sum(Column11 %in% "T")/(length(Column11)-spaces11)
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|
|
438 T12<-sum(Column12 %in% "T")/(length(Column12)-spaces12)
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|
|
439 T13<-sum(Column13 %in% "T")/(length(Column13)-spaces13)
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|
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440 T14<-sum(Column14 %in% "T")/(length(Column14)-spaces14)
|
|
|
441 T15<-sum(Column15 %in% "T")/(length(Column15)-spaces15)
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|
|
442 TllTs<-cbind(T1,T2,T3,T4,T5,T6,T7,T8,T9,T10,T11,T12,T13,T14,T15)
|
|
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443
|
|
|
444
|
|
|
445 V1<-sum(Column1 %in% "V")/(length(Column1)-spaces1)
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|
|
446 V2<-sum(Column2 %in% "V")/(length(Column2)-spaces2)
|
|
|
447 V3<-sum(Column3 %in% "V")/(length(Column3)-spaces3)
|
|
|
448 V4<-sum(Column4 %in% "V")/(length(Column4)-spaces4)
|
|
|
449 V5<-sum(Column5 %in% "V")/(length(Column5)-spaces5)
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|
|
450 V6<-sum(Column6 %in% "V")/(length(Column6)-spaces6)
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|
|
451 V7<-sum(Column7 %in% "V")/(length(Column7)-spaces7)
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|
|
452 V8<-sum(Column8 %in% "V")/(length(Column8)-spaces8)
|
|
|
453 V9<-sum(Column9 %in% "V")/(length(Column9)-spaces9)
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|
|
454 V10<-sum(Column10 %in% "V")/(length(Column10)-spaces10)
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|
|
455 V11<-sum(Column11 %in% "V")/(length(Column11)-spaces11)
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|
|
456 V12<-sum(Column12 %in% "V")/(length(Column12)-spaces12)
|
|
|
457 V13<-sum(Column13 %in% "V")/(length(Column13)-spaces13)
|
|
|
458 V14<-sum(Column14 %in% "V")/(length(Column14)-spaces14)
|
|
|
459 V15<-sum(Column15 %in% "V")/(length(Column15)-spaces15)
|
|
|
460 VllVs<-cbind(V1,V2,V3,V4,V5,V6,V7,V8,V9,V10,V11,V12,V13,V14,V15)
|
|
|
461
|
|
|
462
|
|
|
463 W1<-sum(Column1 %in% "W")/(length(Column1)-spaces1)
|
|
|
464 W2<-sum(Column2 %in% "W")/(length(Column2)-spaces2)
|
|
|
465 W3<-sum(Column3 %in% "W")/(length(Column3)-spaces3)
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|
|
466 W4<-sum(Column4 %in% "W")/(length(Column4)-spaces4)
|
|
|
467 W5<-sum(Column5 %in% "W")/(length(Column5)-spaces5)
|
|
|
468 W6<-sum(Column6 %in% "W")/(length(Column6)-spaces6)
|
|
|
469 W7<-sum(Column7 %in% "W")/(length(Column7)-spaces7)
|
|
|
470 W8<-sum(Column8 %in% "W")/(length(Column8)-spaces8)
|
|
|
471 W9<-sum(Column9 %in% "W")/(length(Column9)-spaces9)
|
|
|
472 W10<-sum(Column10 %in% "W")/(length(Column10)-spaces10)
|
|
|
473 W11<-sum(Column11 %in% "W")/(length(Column11)-spaces11)
|
|
|
474 W12<-sum(Column12 %in% "W")/(length(Column12)-spaces12)
|
|
|
475 W13<-sum(Column13 %in% "W")/(length(Column13)-spaces13)
|
|
|
476 W14<-sum(Column14 %in% "W")/(length(Column14)-spaces14)
|
|
|
477 W15<-sum(Column15 %in% "W")/(length(Column15)-spaces15)
|
|
|
478 WllWs<-cbind(W1,W2,W3,W4,W5,W6,W7,W8,W9,W10,W11,W12,W13,W14,W15)
|
|
|
479
|
|
|
480
|
|
|
481 Y1<-sum(Column1 %in% "Y")/(length(Column1)-spaces1)
|
|
|
482 Y2<-sum(Column2 %in% "Y")/(length(Column2)-spaces2)
|
|
|
483 Y3<-sum(Column3 %in% "Y")/(length(Column3)-spaces3)
|
|
|
484 Y4<-sum(Column4 %in% "Y")/(length(Column4)-spaces4)
|
|
|
485 Y5<-sum(Column5 %in% "Y")/(length(Column5)-spaces5)
|
|
|
486 Y6<-sum(Column6 %in% "Y")/(length(Column6)-spaces6)
|
|
|
487 Y7<-sum(Column7 %in% "Y")/(length(Column7)-spaces7)
|
|
|
488 Y8<-sum(Column8 %in% "Y")/(length(Column8)-spaces8)
|
|
|
489 Y9<-sum(Column9 %in% "Y")/(length(Column9)-spaces9)
|
|
|
490 Y10<-sum(Column10 %in% "Y")/(length(Column10)-spaces10)
|
|
|
491 Y11<-sum(Column11 %in% "Y")/(length(Column11)-spaces11)
|
|
|
492 Y12<-sum(Column12 %in% "Y")/(length(Column12)-spaces12)
|
|
|
493 Y13<-sum(Column13 %in% "Y")/(length(Column13)-spaces13)
|
|
|
494 Y14<-sum(Column14 %in% "Y")/(length(Column14)-spaces14)
|
|
|
495 Y15<-sum(Column15 %in% "Y")/(length(Column15)-spaces15)
|
|
|
496 YllYs<-cbind(Y1,Y2,Y3,Y4,Y5,Y6,Y7,Y8,Y9,Y10,Y11,Y12,Y13,Y14,Y15)
|
|
|
497 }
|
|
|
498 #this is substrate percents
|
|
|
499
|
|
|
500 #A C D E F G H I K L N P Q R S T V W Y
|
|
|
501
|
|
|
502 PercentTable<-rbind(AllAs,CllCs,DllDs,EllEs,FllFs,GllGs,HllHs,IllIs,KllKs,LllLs,MllMs,NllNs,PllPs,QllQs,RllRs,SllSs,TllTs,VllVs,WllWs,YllYs)
|
|
|
503 PercentTable<-PercentTable*100
|
|
|
504
|
|
|
505 #create the SD table
|
|
|
506 SDtable<-matrix(data = rep(1,times=(nrow(PercentTable)*ncol(PercentTable))),nrow = nrow(PercentTable),ncol = ncol(PercentTable))
|
|
|
507 #for every row, a percertage minus the same mean over the same SD
|
|
|
508 if(1==1){
|
|
|
509 SDtable[1,]<-(PercentTable[1,]-Amean)/Asd
|
|
|
510 SDtable[2,]<-(PercentTable[2,]-Cmean)/Csd
|
|
|
511 SDtable[3,]<-(PercentTable[3,]-Dmean)/Dsd
|
|
|
512 SDtable[4,]<-(PercentTable[4,]-Emean)/Esd
|
|
|
513 SDtable[5,]<-(PercentTable[5,]-Fmean)/Fsd
|
|
|
514 SDtable[6,]<-(PercentTable[6,]-Gmean)/Gsd
|
|
|
515 SDtable[7,]<-(PercentTable[7,]-Hmean)/Hsd
|
|
|
516 SDtable[8,]<-(PercentTable[8,]-Imean)/Isd
|
|
|
517 SDtable[9,]<-(PercentTable[9,]-Kmean)/Ksd
|
|
|
518 SDtable[10,]<-(PercentTable[10,]-Lmean)/Lsd
|
|
|
519 SDtable[11,]<-(PercentTable[11,]-Mmean)/Msd
|
|
|
520 SDtable[12,]<-(PercentTable[12,]-Nmean)/Nsd
|
|
|
521 SDtable[13,]<-(PercentTable[13,]-Pmean)/Psd
|
|
|
522 SDtable[14,]<-(PercentTable[14,]-Qmean)/Qsd
|
|
|
523 SDtable[15,]<-(PercentTable[15,]-Rmean)/Rsd
|
|
|
524 SDtable[16,]<-(PercentTable[16,]-Smean)/Ssd
|
|
|
525 SDtable[17,]<-(PercentTable[17,]-Tmean)/Tsd
|
|
|
526 SDtable[18,]<-(PercentTable[18,]-Vmean)/Vsd
|
|
|
527 SDtable[19,]<-(PercentTable[19,]-Wmean)/Wsd
|
|
|
528 SDtable[20,]<-(PercentTable[20,]-Ymean)/Ysd
|
|
|
529 }
|
|
|
530
|
|
|
531
|
|
|
532 SetOfAAs<-c("Letter","A","C","D","E","F","G","H","I","K","L","M","N","P","Q","R","S","T","V","W","Y")
|
|
|
533
|
|
|
534 SumOfSigmaAAs<-c(1:15)
|
|
|
535
|
|
|
536 for (i in 1:15){
|
|
|
537 SumOfSigmasValue<-0
|
|
|
538 for (j in 1:20){
|
|
|
539 value<-0
|
|
|
540 if (SDtable[j,i]>2){
|
|
|
541 q=j+1
|
|
|
542 value<-sum(substrates[,i]==SetOfAAs[q])
|
|
|
543 }
|
|
|
544 SumOfSigmasValue<-SumOfSigmasValue+value
|
|
|
545 }
|
|
|
546 SumOfSigmaAAs[i]<-SumOfSigmasValue
|
|
|
547 }
|
|
|
548
|
|
|
549 AAs1<-length(substrates[,1])-sum(substrates[,1]=="")
|
|
|
550 AAs2<-length(substrates[,2])-sum(substrates[,2]=="")
|
|
|
551 AAs3<-length(substrates[,3])-sum(substrates[,3]=="")
|
|
|
552 AAs4<-length(substrates[,4])-sum(substrates[,4]=="")
|
|
|
553 AAs5<-length(substrates[,5])-sum(substrates[,5]=="")
|
|
|
554 AAs6<-length(substrates[,6])-sum(substrates[,6]=="")
|
|
|
555 AAs7<-length(substrates[,7])-sum(substrates[,7]=="")
|
|
|
556 AAs8<-length(substrates[,8])-sum(substrates[,8]=="")
|
|
|
557 AAs9<-length(substrates[,9])-sum(substrates[,9]=="")
|
|
|
558 AAs10<-length(substrates[,10])-sum(substrates[,10]=="")
|
|
|
559 AAs11<-length(substrates[,11])-sum(substrates[,11]=="")
|
|
|
560 AAs12<-length(substrates[,12])-sum(substrates[,12]=="")
|
|
|
561 AAs13<-length(substrates[,13])-sum(substrates[,13]=="")
|
|
|
562 AAs14<-length(substrates[,14])-sum(substrates[,14]=="")
|
|
|
563 AAs15<-length(substrates[,15])-sum(substrates[,15]=="")
|
|
|
564
|
|
|
565 AAsAtPositions<-c(AAs1,AAs2,AAs3,AAs4,AAs5,AAs6,AAs7,AAs8,AAs9,AAs10,AAs11,AAs12,AAs13,AAs14,AAs15)
|
|
|
566 # AAsAtPositions<-c(length(substrates[,1]),length(substrates[,2]),length(substrates[,3]),length(substrates[,4]),
|
|
|
567 # length(substrates[,5]),length(substrates[,6]),length(substrates[,7]),length(substrates[,8]),
|
|
|
568 # length(substrates[,9]))
|
|
|
569
|
|
|
570 SumOfExpectedSigmaAAs<-c(1:15)
|
|
|
571 for (i in 1:15){
|
|
|
572 ExpectedValue<-0
|
|
|
573 for (j in 1:20){
|
|
|
574 value<-0
|
|
|
575 if (SDtable[j,i]>2){
|
|
|
576 value<-AllMeans[j]
|
|
|
577 }
|
|
|
578 ExpectedValue<-ExpectedValue+value
|
|
|
579 }
|
|
|
580 SumOfExpectedSigmaAAs[i]<-ExpectedValue*(length(substrates[,i])-sum(substrates[,i]%in% ""))/100
|
|
|
581 }
|
|
|
582
|
|
|
583 #SelectivityRow<-SumOfSigmaAAs/SumOfExpectedSigmaAAs
|
|
|
584
|
|
|
585 SelectivityRow<-rep(0,times=15)
|
|
|
586
|
|
|
587 for (q in 1:15) {
|
|
|
588 SelectivityRow[q]<-(SumOfSigmaAAs[q]/SumOfExpectedSigmaAAs[q])*(SumOfSigmaAAs[q]/AAsAtPositions[q])
|
|
|
589 }
|
|
|
590
|
|
|
591 SelectivitySheet<-rbind(SumOfSigmaAAs,SumOfExpectedSigmaAAs,SelectivityRow)
|
|
|
592
|
|
|
593 SetOfAAs<-matrix(data = SetOfAAs,ncol = 1)
|
|
|
594 SDtableu<-SDtable
|
|
|
595 HeaderSD<-c(-7:7)
|
|
|
596 SDtable<-rbind(HeaderSD,SDtableu)
|
|
|
597 row.names(SDtable)<-NULL
|
|
|
598 SDtable<-data.frame(SetOfAAs,SDtable)
|
|
|
599
|
|
|
600 PercentTable<-rbind(HeaderSD,PercentTable)
|
|
|
601 row.names(PercentTable)<-NULL
|
|
|
602 PercentTable<-data.frame(SetOfAAs,PercentTable)
|
|
|
603 numberofY<-as.numeric(SubstrateBackgroundFrequency[,34])
|
|
|
604 numberofY<-numberofY[!is.na(numberofY)]
|
|
|
605
|
|
|
606 numberofPY<-as.numeric(SubstrateBackgroundFrequency[,35])
|
|
|
607 numberofPY<-numberofPY[!is.na(numberofPY)]
|
|
|
608
|
|
|
609 NormalizationScore<-sum(numberofPY)/sum(numberofY)
|
|
|
610
|
|
|
611 # positions<-matrix(data = NA, nrow=20,ncol = 15)
|
|
|
612 #
|
|
|
613 # #column1
|
|
|
614 #
|
|
|
615 # for (q in 1:15) {
|
|
|
616 # sA<-sum(substrates[,i]=="A")
|
|
|
617 # positions[1,i]<-sA
|
|
|
618 # sC<-sum(substrates[,i]=="C")
|
|
|
619 # positions[2,i]<-sC
|
|
|
620 # sD<-sum(substrates[,i]=="D")
|
|
|
621 # positions[3,i]<-sD
|
|
|
622 # sE<-sum(substrates[,i]=="E")
|
|
|
623 # positions[4,i]<-sE
|
|
|
624 # sF<-sum(substrates[,i]=="F")
|
|
|
625 # sG<-sum(substrates[,i]=="G")
|
|
|
626 # sH<-sum(substrates[,i]=="H")
|
|
|
627 # sI<-sum(substrates[,i]=="I")
|
|
|
628 # sK<-sum(substrates[,i]=="K")
|
|
|
629 # sL<-sum(substrates[,i]=="L")
|
|
|
630 # sM<-sum(substrates[,i]=="M")
|
|
|
631 # sN<-sum(substrates[,i]=="N")
|
|
|
632 # sP<-sum(substrates[,i]=="P")
|
|
|
633 # sQ<-sum(substrates[,i]=="Q")
|
|
|
634 # sR<-sum(substrates[,i]=="R")
|
|
|
635 # sS<-sum(substrates[,i]=="S")
|
|
|
636 # sT<-sum(substrates[,i]=="T")
|
|
|
637 # sV<-sum(substrates[,i]=="V")
|
|
|
638 # sW<-sum(substrates[,i]=="W")
|
|
|
639 # sY<-sum(substrates[,i]=="Y")
|
|
|
640 # positions[5,i]<-sF
|
|
|
641 # positions[6,i]<-sG
|
|
|
642 # positions[7,i]<-sH
|
|
|
643 # positions[8,i]<-sI
|
|
|
644 # positions[9,i]<-sK
|
|
|
645 # positions[10,i]<-sL
|
|
|
646 # positions[11,i]<-sM
|
|
|
647 # positions[12,i]<-sN
|
|
|
648 # positions[13,i]<-sP
|
|
|
649 # positions[14,i]<-sQ
|
|
|
650 # positions[15,i]<-sR
|
|
|
651 # positions[16,i]<-sS
|
|
|
652 # positions[17,i]<-sT
|
|
|
653 # positions[18,i]<-sV
|
|
|
654 # positions[19,i]<-sW
|
|
|
655 # positions[20,i]<-sY
|
|
|
656 # }
|
|
|
657
|
|
|
658 #here I create the positions table which is needed for the endogenous prob matrix and is simply "how many times did an AA show up in this spot?
|
|
|
659 if (6==6){
|
|
|
660 Column1<-substrates[,1]
|
|
|
661 Column2<-substrates[,2]
|
|
|
662 Column3<-substrates[,3]
|
|
|
663 Column4<-substrates[,4]
|
|
|
664 Column5<-substrates[,5]
|
|
|
665 Column6<-substrates[,6]
|
|
|
666 Column7<-substrates[,7]
|
|
|
667 Column8<-substrates[,8]
|
|
|
668 Column9<-substrates[,9]
|
|
|
669 Column10<-substrates[,10]
|
|
|
670 Column11<-substrates[,11]
|
|
|
671 Column12<-substrates[,12]
|
|
|
672 Column13<-substrates[,13]
|
|
|
673 Column14<-substrates[,14]
|
|
|
674 Column15<-substrates[,15]
|
|
|
675
|
|
|
676 spaces1<-sum((Column1%in% ""))
|
|
|
677 spaces2<-sum(Column2%in% "")
|
|
|
678 spaces3<-sum(Column3%in% "")
|
|
|
679 spaces4<-sum(Column4%in% "")
|
|
|
680 spaces5<-sum(Column5%in% "")
|
|
|
681 spaces6<-sum(Column6%in% "")
|
|
|
682 spaces7<-sum(Column7%in% "")
|
|
|
683 spaces8<-sum(Column8%in% "")
|
|
|
684 spaces9<-sum(Column9%in% "")
|
|
|
685 spaces10<-sum(Column10%in% "")
|
|
|
686 spaces11<-sum(Column11%in% "")
|
|
|
687 spaces12<-sum(Column12%in% "")
|
|
|
688 spaces13<-sum(Column13%in% "")
|
|
|
689 spaces14<-sum(Column14%in% "")
|
|
|
690 spaces15<-sum(Column15%in% "")
|
|
|
691
|
|
|
692 A1<-sum(Column1 %in% "A")
|
|
|
693 A2<-sum(Column2 %in% "A")
|
|
|
694 A3<-sum(Column3 %in% "A")
|
|
|
695 A4<-sum(Column4 %in% "A")
|
|
|
696 A5<-sum(Column5 %in% "A")
|
|
|
697 A6<-sum(Column6 %in% "A")
|
|
|
698 A7<-sum(Column7 %in% "A")
|
|
|
699 A8<-sum(Column8 %in% "A")
|
|
|
700 A9<-sum(Column9 %in% "A")
|
|
|
701 A10<-sum(Column10 %in% "A")
|
|
|
702 A11<-sum(Column11 %in% "A")
|
|
|
703 A12<-sum(Column12 %in% "A")
|
|
|
704 A13<-sum(Column13 %in% "A")
|
|
|
705 A14<-sum(Column14 %in% "A")
|
|
|
706 A15<-sum(Column15 %in% "A")
|
|
|
707 AllAs<-cbind(A1,A2,A3,A4,A5,A6,A7,A8,A9,A10,A11,A12,A13,A14,A15)
|
|
|
708
|
|
|
709 C1<-sum(Column1 %in% "C")
|
|
|
710 C2<-sum(Column2 %in% "C")
|
|
|
711 C3<-sum(Column3 %in% "C")
|
|
|
712 C4<-sum(Column4 %in% "C")
|
|
|
713 C5<-sum(Column5 %in% "C")
|
|
|
714 C6<-sum(Column6 %in% "C")
|
|
|
715 C7<-sum(Column7 %in% "C")
|
|
|
716 C8<-sum(Column8 %in% "C")
|
|
|
717 C9<-sum(Column9 %in% "C")
|
|
|
718 C10<-sum(Column10 %in% "C")
|
|
|
719 C11<-sum(Column11 %in% "C")
|
|
|
720 C12<-sum(Column12 %in% "C")
|
|
|
721 C13<-sum(Column13 %in% "C")
|
|
|
722 C14<-sum(Column14 %in% "C")
|
|
|
723 C15<-sum(Column15 %in% "C")
|
|
|
724 CllCs<-cbind(C1,C2,C3,C4,C5,C6,C7,C8,C9,C10,C11,C12,C13,C14,C15)
|
|
|
725
|
|
|
726 D1<-sum(Column1 %in% "D")
|
|
|
727 D2<-sum(Column2 %in% "D")
|
|
|
728 D3<-sum(Column3 %in% "D")
|
|
|
729 D4<-sum(Column4 %in% "D")
|
|
|
730 D5<-sum(Column5 %in% "D")
|
|
|
731 D6<-sum(Column6 %in% "D")
|
|
|
732 D7<-sum(Column7 %in% "D")
|
|
|
733 D8<-sum(Column8 %in% "D")
|
|
|
734 D9<-sum(Column9 %in% "D")
|
|
|
735 D10<-sum(Column10 %in% "D")
|
|
|
736 D11<-sum(Column11 %in% "D")
|
|
|
737 D12<-sum(Column12 %in% "D")
|
|
|
738 D13<-sum(Column13 %in% "D")
|
|
|
739 D14<-sum(Column14 %in% "D")
|
|
|
740 D15<-sum(Column15 %in% "D")
|
|
|
741 DllDs<-cbind(D1,D2,D3,D4,D5,D6,D7,D8,D9,D10,D11,D12,D13,D14,D15)
|
|
|
742
|
|
|
743 E1<-sum(Column1 %in% "E")
|
|
|
744 E2<-sum(Column2 %in% "E")
|
|
|
745 E3<-sum(Column3 %in% "E")
|
|
|
746 E4<-sum(Column4 %in% "E")
|
|
|
747 E5<-sum(Column5 %in% "E")
|
|
|
748 E6<-sum(Column6 %in% "E")
|
|
|
749 E7<-sum(Column7 %in% "E")
|
|
|
750 E8<-sum(Column8 %in% "E")
|
|
|
751 E9<-sum(Column9 %in% "E")
|
|
|
752 E10<-sum(Column10 %in% "E")
|
|
|
753 E11<-sum(Column11 %in% "E")
|
|
|
754 E12<-sum(Column12 %in% "E")
|
|
|
755 E13<-sum(Column13 %in% "E")
|
|
|
756 E14<-sum(Column14 %in% "E")
|
|
|
757 E15<-sum(Column15 %in% "E")
|
|
|
758 EllEs<-cbind(E1,E2,E3,E4,E5,E6,E7,E8,E9,E10,E11,E12,E13,E14,E15)
|
|
|
759
|
|
|
760 F1<-sum(Column1 %in% "F")
|
|
|
761 F2<-sum(Column2 %in% "F")
|
|
|
762 F3<-sum(Column3 %in% "F")
|
|
|
763 F4<-sum(Column4 %in% "F")
|
|
|
764 F5<-sum(Column5 %in% "F")
|
|
|
765 F6<-sum(Column6 %in% "F")
|
|
|
766 F7<-sum(Column7 %in% "F")
|
|
|
767 F8<-sum(Column8 %in% "F")
|
|
|
768 F9<-sum(Column9 %in% "F")
|
|
|
769 F10<-sum(Column10 %in% "F")
|
|
|
770 F11<-sum(Column11 %in% "F")
|
|
|
771 F12<-sum(Column12 %in% "F")
|
|
|
772 F13<-sum(Column13 %in% "F")
|
|
|
773 F14<-sum(Column14 %in% "F")
|
|
|
774 F15<-sum(Column15 %in% "F")
|
|
|
775 FllFs<-cbind(F1,F2,F3,F4,F5,F6,F7,F8,F9,F10,F11,F12,F13,F14,F15)
|
|
|
776
|
|
|
777 G1<-sum(Column1 %in% "G")
|
|
|
778 G2<-sum(Column2 %in% "G")
|
|
|
779 G3<-sum(Column3 %in% "G")
|
|
|
780 G4<-sum(Column4 %in% "G")
|
|
|
781 G5<-sum(Column5 %in% "G")
|
|
|
782 G6<-sum(Column6 %in% "G")
|
|
|
783 G7<-sum(Column7 %in% "G")
|
|
|
784 G8<-sum(Column8 %in% "G")
|
|
|
785 G9<-sum(Column9 %in% "G")
|
|
|
786 G10<-sum(Column10 %in% "G")
|
|
|
787 G11<-sum(Column11 %in% "G")
|
|
|
788 G12<-sum(Column12 %in% "G")
|
|
|
789 G13<-sum(Column13 %in% "G")
|
|
|
790 G14<-sum(Column14 %in% "G")
|
|
|
791 G15<-sum(Column15 %in% "G")
|
|
|
792 GllGs<-cbind(G1,G2,G3,G4,G5,G6,G7,G8,G9,G10,G11,G12,G13,G14,G15)
|
|
|
793
|
|
|
794 H1<-sum(Column1 %in% "H")
|
|
|
795 H2<-sum(Column2 %in% "H")
|
|
|
796 H3<-sum(Column3 %in% "H")
|
|
|
797 H4<-sum(Column4 %in% "H")
|
|
|
798 H5<-sum(Column5 %in% "H")
|
|
|
799 H6<-sum(Column6 %in% "H")
|
|
|
800 H7<-sum(Column7 %in% "H")
|
|
|
801 H8<-sum(Column8 %in% "H")
|
|
|
802 H9<-sum(Column9 %in% "H")
|
|
|
803 H10<-sum(Column10 %in% "H")
|
|
|
804 H11<-sum(Column11 %in% "H")
|
|
|
805 H12<-sum(Column12 %in% "H")
|
|
|
806 H13<-sum(Column13 %in% "H")
|
|
|
807 H14<-sum(Column14 %in% "H")
|
|
|
808 H15<-sum(Column15 %in% "H")
|
|
|
809 HllHs<-cbind(H1,H2,H3,H4,H5,H6,H7,H8,H9,H10,H11,H12,H13,H14,H15)
|
|
|
810
|
|
|
811 I1<-sum(Column1 %in% "I")
|
|
|
812 I2<-sum(Column2 %in% "I")
|
|
|
813 I3<-sum(Column3 %in% "I")
|
|
|
814 I4<-sum(Column4 %in% "I")
|
|
|
815 I5<-sum(Column5 %in% "I")
|
|
|
816 I6<-sum(Column6 %in% "I")
|
|
|
817 I7<-sum(Column7 %in% "I")
|
|
|
818 I8<-sum(Column8 %in% "I")
|
|
|
819 I9<-sum(Column9 %in% "I")
|
|
|
820 I10<-sum(Column10 %in% "I")
|
|
|
821 I11<-sum(Column11 %in% "I")
|
|
|
822 I12<-sum(Column12 %in% "I")
|
|
|
823 I13<-sum(Column13 %in% "I")
|
|
|
824 I14<-sum(Column14 %in% "I")
|
|
|
825 I15<-sum(Column15 %in% "I")
|
|
|
826 IllIs<-cbind(I1,I2,I3,I4,I5,I6,I7,I8,I9,I10,I11,I12,I13,I14,I15)
|
|
|
827
|
|
|
828 K1<-sum(Column1 %in% "K")
|
|
|
829 K2<-sum(Column2 %in% "K")
|
|
|
830 K3<-sum(Column3 %in% "K")
|
|
|
831 K4<-sum(Column4 %in% "K")
|
|
|
832 K5<-sum(Column5 %in% "K")
|
|
|
833 K6<-sum(Column6 %in% "K")
|
|
|
834 K7<-sum(Column7 %in% "K")
|
|
|
835 K8<-sum(Column8 %in% "K")
|
|
|
836 K9<-sum(Column9 %in% "K")
|
|
|
837 K10<-sum(Column10 %in% "K")
|
|
|
838 K11<-sum(Column11 %in% "K")
|
|
|
839 K12<-sum(Column12 %in% "K")
|
|
|
840 K13<-sum(Column13 %in% "K")
|
|
|
841 K14<-sum(Column14 %in% "K")
|
|
|
842 K15<-sum(Column15 %in% "K")
|
|
|
843 KllKs<-cbind(K1,K2,K3,K4,K5,K6,K7,K8,K9,K10,K11,K12,K13,K14,K15)
|
|
|
844
|
|
|
845 L1<-sum(Column1 %in% "L")
|
|
|
846 L2<-sum(Column2 %in% "L")
|
|
|
847 L3<-sum(Column3 %in% "L")
|
|
|
848 L4<-sum(Column4 %in% "L")
|
|
|
849 L5<-sum(Column5 %in% "L")
|
|
|
850 L6<-sum(Column6 %in% "L")
|
|
|
851 L7<-sum(Column7 %in% "L")
|
|
|
852 L8<-sum(Column8 %in% "L")
|
|
|
853 L9<-sum(Column9 %in% "L")
|
|
|
854 L10<-sum(Column10 %in% "L")
|
|
|
855 L11<-sum(Column11 %in% "L")
|
|
|
856 L12<-sum(Column12 %in% "L")
|
|
|
857 L13<-sum(Column13 %in% "L")
|
|
|
858 L14<-sum(Column14 %in% "L")
|
|
|
859 L15<-sum(Column15 %in% "L")
|
|
|
860 LllLs<-cbind(L1,L2,L3,L4,L5,L6,L7,L8,L9,L10,L11,L12,L13,L14,L15)
|
|
|
861
|
|
|
862 M1<-sum(Column1 %in% "M")
|
|
|
863 M2<-sum(Column2 %in% "M")
|
|
|
864 M3<-sum(Column3 %in% "M")
|
|
|
865 M4<-sum(Column4 %in% "M")
|
|
|
866 M5<-sum(Column5 %in% "M")
|
|
|
867 M6<-sum(Column6 %in% "M")
|
|
|
868 M7<-sum(Column7 %in% "M")
|
|
|
869 M8<-sum(Column8 %in% "M")
|
|
|
870 M9<-sum(Column9 %in% "M")
|
|
|
871 M10<-sum(Column10 %in% "M")
|
|
|
872 M11<-sum(Column11 %in% "M")
|
|
|
873 M12<-sum(Column12 %in% "M")
|
|
|
874 M13<-sum(Column13 %in% "M")
|
|
|
875 M14<-sum(Column14 %in% "M")
|
|
|
876 M15<-sum(Column15 %in% "M")
|
|
|
877 MllMs<-cbind(M1,M2,M3,M4,M5,M6,M7,M8,M9,M10,M11,M12,M13,M14,M15)
|
|
|
878
|
|
|
879 N1<-sum(Column1 %in% "N")
|
|
|
880 N2<-sum(Column2 %in% "N")
|
|
|
881 N3<-sum(Column3 %in% "N")
|
|
|
882 N4<-sum(Column4 %in% "N")
|
|
|
883 N5<-sum(Column5 %in% "N")
|
|
|
884 N6<-sum(Column6 %in% "N")
|
|
|
885 N7<-sum(Column7 %in% "N")
|
|
|
886 N8<-sum(Column8 %in% "N")
|
|
|
887 N9<-sum(Column9 %in% "N")
|
|
|
888 N10<-sum(Column10 %in% "N")
|
|
|
889 N11<-sum(Column11 %in% "N")
|
|
|
890 N12<-sum(Column12 %in% "N")
|
|
|
891 N13<-sum(Column13 %in% "N")
|
|
|
892 N14<-sum(Column14 %in% "N")
|
|
|
893 N15<-sum(Column15 %in% "N")
|
|
|
894 NllNs<-cbind(N1,N2,N3,N4,N5,N6,N7,N8,N9,N10,N11,N12,N13,N14,N15)
|
|
|
895
|
|
|
896 P1<-sum(Column1 %in% "P")
|
|
|
897 P2<-sum(Column2 %in% "P")
|
|
|
898 P3<-sum(Column3 %in% "P")
|
|
|
899 P4<-sum(Column4 %in% "P")
|
|
|
900 P5<-sum(Column5 %in% "P")
|
|
|
901 P6<-sum(Column6 %in% "P")
|
|
|
902 P7<-sum(Column7 %in% "P")
|
|
|
903 P8<-sum(Column8 %in% "P")
|
|
|
904 P9<-sum(Column9 %in% "P")
|
|
|
905 P10<-sum(Column10 %in% "P")
|
|
|
906 P11<-sum(Column11 %in% "P")
|
|
|
907 P12<-sum(Column12 %in% "P")
|
|
|
908 P13<-sum(Column13 %in% "P")
|
|
|
909 P14<-sum(Column14 %in% "P")
|
|
|
910 P15<-sum(Column15 %in% "P")
|
|
|
911 PllPs<-cbind(P1,P2,P3,P4,P5,P6,P7,P8,P9,P10,P11,P12,P13,P14,P15)
|
|
|
912
|
|
|
913 Q1<-sum(Column1 %in% "Q")
|
|
|
914 Q2<-sum(Column2 %in% "Q")
|
|
|
915 Q3<-sum(Column3 %in% "Q")
|
|
|
916 Q4<-sum(Column4 %in% "Q")
|
|
|
917 Q5<-sum(Column5 %in% "Q")
|
|
|
918 Q6<-sum(Column6 %in% "Q")
|
|
|
919 Q7<-sum(Column7 %in% "Q")
|
|
|
920 Q8<-sum(Column8 %in% "Q")
|
|
|
921 Q9<-sum(Column9 %in% "Q")
|
|
|
922 Q10<-sum(Column10 %in% "Q")
|
|
|
923 Q11<-sum(Column11 %in% "Q")
|
|
|
924 Q12<-sum(Column12 %in% "Q")
|
|
|
925 Q13<-sum(Column13 %in% "Q")
|
|
|
926 Q14<-sum(Column14 %in% "Q")
|
|
|
927 Q15<-sum(Column15 %in% "Q")
|
|
|
928 QllQs<-cbind(Q1,Q2,Q3,Q4,Q5,Q6,Q7,Q8,Q9,Q10,Q11,Q12,Q13,Q14,Q15)
|
|
|
929
|
|
|
930 R1<-sum(Column1 %in% "R")
|
|
|
931 R2<-sum(Column2 %in% "R")
|
|
|
932 R3<-sum(Column3 %in% "R")
|
|
|
933 R4<-sum(Column4 %in% "R")
|
|
|
934 R5<-sum(Column5 %in% "R")
|
|
|
935 R6<-sum(Column6 %in% "R")
|
|
|
936 R7<-sum(Column7 %in% "R")
|
|
|
937 R8<-sum(Column8 %in% "R")
|
|
|
938 R9<-sum(Column9 %in% "R")
|
|
|
939 R10<-sum(Column10 %in% "R")
|
|
|
940 R11<-sum(Column11 %in% "R")
|
|
|
941 R12<-sum(Column12 %in% "R")
|
|
|
942 R13<-sum(Column13 %in% "R")
|
|
|
943 R14<-sum(Column14 %in% "R")
|
|
|
944 R15<-sum(Column15 %in% "R")
|
|
|
945 RllRs<-cbind(R1,R2,R3,R4,R5,R6,R7,R8,R9,R10,R11,R12,R13,R14,R15)
|
|
|
946
|
|
|
947 S1<-sum(Column1 %in% "S")
|
|
|
948 S2<-sum(Column2 %in% "S")
|
|
|
949 S3<-sum(Column3 %in% "S")
|
|
|
950 S4<-sum(Column4 %in% "S")
|
|
|
951 S5<-sum(Column5 %in% "S")
|
|
|
952 S6<-sum(Column6 %in% "S")
|
|
|
953 S7<-sum(Column7 %in% "S")
|
|
|
954 S8<-sum(Column8 %in% "S")
|
|
|
955 S9<-sum(Column9 %in% "S")
|
|
|
956 S10<-sum(Column10 %in% "S")
|
|
|
957 S11<-sum(Column11 %in% "S")
|
|
|
958 S12<-sum(Column12 %in% "S")
|
|
|
959 S13<-sum(Column13 %in% "S")
|
|
|
960 S14<-sum(Column14 %in% "S")
|
|
|
961 S15<-sum(Column15 %in% "S")
|
|
|
962 SllSs<-cbind(S1,S2,S3,S4,S5,S6,S7,S8,S9,S10,S11,S12,S13,S14,S15)
|
|
|
963
|
|
|
964 T1<-sum(Column1 %in% "T")
|
|
|
965 T2<-sum(Column2 %in% "T")
|
|
|
966 T3<-sum(Column3 %in% "T")
|
|
|
967 T4<-sum(Column4 %in% "T")
|
|
|
968 T5<-sum(Column5 %in% "T")
|
|
|
969 T6<-sum(Column6 %in% "T")
|
|
|
970 T7<-sum(Column7 %in% "T")
|
|
|
971 T8<-sum(Column8 %in% "T")
|
|
|
972 T9<-sum(Column9 %in% "T")
|
|
|
973 T10<-sum(Column10 %in% "T")
|
|
|
974 T11<-sum(Column11 %in% "T")
|
|
|
975 T12<-sum(Column12 %in% "T")
|
|
|
976 T13<-sum(Column13 %in% "T")
|
|
|
977 T14<-sum(Column14 %in% "T")
|
|
|
978 T15<-sum(Column15 %in% "T")
|
|
|
979 TllTs<-cbind(T1,T2,T3,T4,T5,T6,T7,T8,T9,T10,T11,T12,T13,T14,T15)
|
|
|
980
|
|
|
981 V1<-sum(Column1 %in% "V")
|
|
|
982 V2<-sum(Column2 %in% "V")
|
|
|
983 V3<-sum(Column3 %in% "V")
|
|
|
984 V4<-sum(Column4 %in% "V")
|
|
|
985 V5<-sum(Column5 %in% "V")
|
|
|
986 V6<-sum(Column6 %in% "V")
|
|
|
987 V7<-sum(Column7 %in% "V")
|
|
|
988 V8<-sum(Column8 %in% "V")
|
|
|
989 V9<-sum(Column9 %in% "V")
|
|
|
990 V10<-sum(Column10 %in% "V")
|
|
|
991 V11<-sum(Column11 %in% "V")
|
|
|
992 V12<-sum(Column12 %in% "V")
|
|
|
993 V13<-sum(Column13 %in% "V")
|
|
|
994 V14<-sum(Column14 %in% "V")
|
|
|
995 V15<-sum(Column15 %in% "V")
|
|
|
996 VllVs<-cbind(V1,V2,V3,V4,V5,V6,V7,V8,V9,V10,V11,V12,V13,V14,V15)
|
|
|
997
|
|
|
998 W1<-sum(Column1 %in% "W")
|
|
|
999 W2<-sum(Column2 %in% "W")
|
|
|
1000 W3<-sum(Column3 %in% "W")
|
|
|
1001 W4<-sum(Column4 %in% "W")
|
|
|
1002 W5<-sum(Column5 %in% "W")
|
|
|
1003 W6<-sum(Column6 %in% "W")
|
|
|
1004 W7<-sum(Column7 %in% "W")
|
|
|
1005 W8<-sum(Column8 %in% "W")
|
|
|
1006 W9<-sum(Column9 %in% "W")
|
|
|
1007 W10<-sum(Column10 %in% "W")
|
|
|
1008 W11<-sum(Column11 %in% "W")
|
|
|
1009 W12<-sum(Column12 %in% "W")
|
|
|
1010 W13<-sum(Column13 %in% "W")
|
|
|
1011 W14<-sum(Column14 %in% "W")
|
|
|
1012 W15<-sum(Column15 %in% "W")
|
|
|
1013 WllWs<-cbind(W1,W2,W3,W4,W5,W6,W7,W8,W9,W10,W11,W12,W13,W14,W15)
|
|
|
1014
|
|
|
1015 Y1<-sum(Column1 %in% "Y")
|
|
|
1016 Y2<-sum(Column2 %in% "Y")
|
|
|
1017 Y3<-sum(Column3 %in% "Y")
|
|
|
1018 Y4<-sum(Column4 %in% "Y")
|
|
|
1019 Y5<-sum(Column5 %in% "Y")
|
|
|
1020 Y6<-sum(Column6 %in% "Y")
|
|
|
1021 Y7<-sum(Column7 %in% "Y")
|
|
|
1022 Y8<-sum(Column8 %in% "Y")
|
|
|
1023 Y9<-sum(Column9 %in% "Y")
|
|
|
1024 Y10<-sum(Column10 %in% "Y")
|
|
|
1025 Y11<-sum(Column11 %in% "Y")
|
|
|
1026 Y12<-sum(Column12 %in% "Y")
|
|
|
1027 Y13<-sum(Column13 %in% "Y")
|
|
|
1028 Y14<-sum(Column14 %in% "Y")
|
|
|
1029 Y15<-sum(Column15 %in% "Y")
|
|
|
1030 YllYs<-cbind(Y1,Y2,Y3,Y4,Y5,Y6,Y7,Y8,Y9,Y10,Y11,Y12,Y13,Y14,Y15)
|
|
|
1031 PositionTable<-rbind(AllAs,CllCs,DllDs,EllEs,FllFs,GllGs,HllHs,IllIs,KllKs,LllLs,MllMs,NllNs,PllPs,QllQs,RllRs,SllSs,TllTs,VllVs,WllWs,YllYs)
|
|
|
1032 }
|
|
|
1033 #endogenous prob matrix is AA position over subbackfreqmean
|
|
|
1034 dim(PositionTable)
|
|
|
1035 EPMtable<-PositionTable
|
|
|
1036 # EPMtable[1,]<-(PositionTable[1,]/(PositionTable[1,]*.01*Amean))
|
|
|
1037 # EPMtable[2,]<-(PositionTable[2,]/(PositionTable[2,]*.01*Cmean))
|
|
|
1038 # EPMtable[3,]<-(PositionTable[3,]/(PositionTable[3,]*.01*Dmean))
|
|
|
1039 # EPMtable[4,]<-(PositionTable[4,]/(PositionTable[4,]*.01*Emean))
|
|
|
1040 # EPMtable[5,]<-(PositionTable[5,]/(PositionTable[5,]*.01*Fmean))
|
|
|
1041 # EPMtable[6,]<-(PositionTable[6,]/(PositionTable[6,]*.01*Gmean))
|
|
|
1042 # EPMtable[7,]<-(PositionTable[7,]/(PositionTable[7,]*.01*Hmean))
|
|
|
1043 # EPMtable[8,]<-(PositionTable[8,]/(PositionTable[8,]*.01*Imean))
|
|
|
1044 # EPMtable[9,]<-(PositionTable[9,]/(PositionTable[9,]*.01*Kmean))
|
|
|
1045 # EPMtable[10,]<-(PositionTable[10,]/(PositionTable[10,]*.01*Lmean))
|
|
|
1046 # EPMtable[11,]<-(PositionTable[11,]/(PositionTable[11,]*.01*Mmean))
|
|
|
1047 # EPMtable[12,]<-(PositionTable[12,]/(PositionTable[12,]*.01*Nmean))
|
|
|
1048 # EPMtable[13,]<-(PositionTable[13,]/(PositionTable[13,]*.01*Pmean))
|
|
|
1049 # EPMtable[14,]<-(PositionTable[14,]/(PositionTable[14,]*.01*Qmean))
|
|
|
1050 # EPMtable[15,]<-(PositionTable[15,]/(PositionTable[15,]*.01*Rmean))
|
|
|
1051 # EPMtable[16,]<-(PositionTable[16,]/(PositionTable[16,]*.01*Smean))
|
|
|
1052 # EPMtable[17,]<-(PositionTable[17,]/(PositionTable[17,]*.01*Tmean))
|
|
|
1053 # EPMtable[18,]<-(PositionTable[18,]/(PositionTable[18,]*.01*Vmean))
|
|
|
1054 # EPMtable[19,]<-(PositionTable[19,]/(PositionTable[19,]*.01*Wmean))
|
|
|
1055 # EPMtable[20,]<-(PositionTable[20,]/(PositionTable[20,]*.01*Ymean))
|
|
|
1056
|
|
|
1057 columns<-c(length(Column1)-sum(Column1==""),
|
|
|
1058 length(Column2)-sum(Column2==""),
|
|
|
1059 length(Column3)-sum(Column3==""),
|
|
|
1060 length(Column4)-sum(Column4==""),
|
|
|
1061 length(Column5)-sum(Column5==""),
|
|
|
1062 length(Column6)-sum(Column6==""),
|
|
|
1063 length(Column7)-sum(Column7==""),
|
|
|
1064 length(Column8)-sum(Column8==""),
|
|
|
1065 length(Column9)-sum(Column9==""),
|
|
|
1066 length(Column10)-sum(Column10==""),
|
|
|
1067 length(Column11)-sum(Column11==""),
|
|
|
1068 length(Column12)-sum(Column12==""),
|
|
|
1069 length(Column13)-sum(Column13==""),
|
|
|
1070 length(Column14)-sum(Column14==""),
|
|
|
1071 length(Column15)-sum(Column15==""))
|
|
|
1072
|
|
|
1073 for (z in 1:15) {
|
|
|
1074 for (y in 1:20) {
|
|
|
1075 if (PositionTable[y,z]>0){
|
|
|
1076 EPMtable[y,z]<-PositionTable[y,z]/((columns[z]*.01*AllMeans[y]))
|
|
|
1077 }
|
|
|
1078 if (PositionTable[y,z]==0){
|
|
|
1079 EPMtable[y,z]<-(1/columns[z])/((columns[z]*.01*AllMeans[y]))
|
|
|
1080 }
|
|
|
1081 }
|
|
|
1082 }
|
|
|
1083 #here I created the endogenous probability matrix
|
|
|
1084 #now all I need to do is make the program automatically determine which SDs are >2, and then make it perform screener and sorter on those SDs
|
|
|
1085
|
|
|
1086
|
|
|
1087
|
|
|
1088
|
|
|
1089
|
|
|
1090 # write.xlsx(SDtable,file=FILENAME, sheetName = "Standard Deviation Table",col.names = FALSE,row.names = FALSE,append = TRUE)
|
|
|
1091 # write.xlsx(PercentTable,file = FILENAME,sheetName = "Percent Table",col.names = FALSE,row.names = FALSE,append = TRUE)
|
|
|
1092 # write.xlsx(SelectivitySheet,file = FILENAME,sheetName = "Site Selectivity",col.names = FALSE,row.names = FALSE,append = TRUE)
|
|
|
1093 # write.xlsx(EPMtable,file=FILENAME,sheetName = "Endogenous Probability Matrix",col.names = FALSE,row.names = FALSE,append = TRUE)
|
|
|
1094 # write.xlsx(NormalizationScore,file = FILENAME,sheetName = "Normalization Score",col.names = FALSE,row.names = FALSE,append = TRUE)
|
|
|
1095
|
|
|
1096 NormalizationScore<-c("Normalization Score",NormalizationScore)
|
|
|
1097
|
|
|
1098 write.table(x=c("SD Table"),file=FILENAME,append = TRUE,sep=",", row.names = FALSE, col.names = FALSE)
|
|
|
1099 write.table(SDtable,file=FILENAME,append = TRUE,sep=",", row.names = FALSE, col.names = FALSE)
|
|
|
1100 write.table(x=c("Percent Table"),file=FILENAME,append = TRUE,sep=",", row.names = FALSE, col.names = FALSE)
|
|
|
1101 write.table(PercentTable,file=FILENAME, append = TRUE,sep=",",row.names = FALSE, col.names = FALSE)
|
|
|
1102
|
|
|
1103 EPMtableu<-EPMtable
|
|
|
1104 HeaderSD<-c(-7:7)
|
|
|
1105 EPMtableu<-rbind(HeaderSD,EPMtableu)
|
|
|
1106 row.names(EPMtableu)<-NULL
|
|
|
1107 EPMtableu<-data.frame(SetOfAAs,EPMtableu)
|
|
|
1108
|
|
|
1109 write.table("Site Selectivity Matrix", file = FILENAME2, append = TRUE, sep = ",", row.names = FALSE, col.names = FALSE)
|
|
|
1110 SelectivityHeader=matrix(data = c("Position",-7,-6,-5,-4,-3,-2,-1,0,1,2,3,4,5,6,7),nrow = 1)
|
|
|
1111 head<-matrix(data=rep(" ",times=16),nrow = 1)
|
|
|
1112 SelectivityHeader<-rbind(head,SelectivityHeader)
|
|
|
1113
|
|
|
1114 write.table(SelectivityHeader, file = FILENAME2, append = TRUE, sep = ",", row.names = FALSE, col.names = FALSE)
|
|
|
1115 #colnames(SelectivitySheet)<-c("-7","-6","-5","-4","-3","-2","-1","0","1","2","3","4","5","6","7")
|
|
|
1116 write.table(SelectivitySheet,file = FILENAME2, append = TRUE,sep = ",",row.names = TRUE, col.names = FALSE)
|
|
|
1117 write.table(x=c("Endogenous Probability Matrix"),file=FILENAME2,append = TRUE,sep=",", row.names = FALSE, col.names = FALSE)
|
|
|
1118 write.table(EPMtableu,file = FILENAME2, append = TRUE,sep = ",",row.names = FALSE, col.names = FALSE)
|
|
|
1119 write.table(NormalizationScore, file = FILENAME2, append = TRUE,sep = ",",row.names = FALSE, col.names = FALSE)
|
|
|
1120
|
|
|
1121
|
|
|
1122
|
|
|
1123
|
|
|
1124
|
|
|
1125
|
|
|
1126
|
|
|
1127
|
|
|
1128
|
|
|
1129
|
|
|
1130
|
|
|
1131
|
|
|
1132
|
|
|
1133
|
|
|
1134
|
|
|
1135
|
|
|
1136
|
|
|
1137
|
|
|
1138
|
|
|
1139
|
|
|
1140
|
|
|
1141
|
|
|
1142
|
|
|
1143
|
|
|
1144
|
|
|
1145
|
|
|
1146
|
|
|
1147
|
|
|
1148
|
|
|
1149
|
|
|
1150 #test myself: this script should take in amino acids for each of the 9 positions and give out every single combination of those AAs
|
|
|
1151
|
|
|
1152 #need to do following: fix it so that the accession numbers stay with the substrates,
|
|
|
1153 #also the neg false constant is totaly unphos'd Ys found by FASTA-2-CSV system# uniprot
|
|
|
1154
|
|
|
1155 #HOW MANY: IF THERE'S two aas in each position you get 2^9, so I assume the numbers are:
|
|
|
1156 #(number in position-4)*(number in position -3)*(number in position -2)...=total
|
|
|
1157 # require(rJava)
|
|
|
1158 # require(xlsxjars)
|
|
|
1159 # require(xlsx)
|
|
|
1160 # # require(readxl)
|
|
|
1161
|
|
|
1162 #View(SDtable)
|
|
|
1163 bareSDs<-SDtable[2:21,2:16]
|
|
|
1164 goodones<-bareSDs>2
|
|
|
1165
|
|
|
1166 # Positionm7<-which(goodones[,1] %in% TRUE)
|
|
|
1167 # if (length(Positionm7)<1){Positionm7<-which(bareSDs[,1]==max(bareSDs[,1]))}
|
|
|
1168 # Positionm6<-which(goodones[,2] %in% TRUE)
|
|
|
1169 # if (length(Positionm6)<1){Positionm6<-which(bareSDs[,2]==max(bareSDs[,2]))}
|
|
|
1170 # Positionm5<-which(goodones[,3] %in% TRUE)
|
|
|
1171 # if (length(Positionm5)<1){Positionm5<-which(bareSDs[,3]==max(bareSDs[,3]))}
|
|
|
1172 # Positionm4<-which(goodones[,4] %in% TRUE)
|
|
|
1173 # if (length(Positionm4)<2){Positionm4<-bareSDs[,4][order(bareSDs[,4])[1:2]]}
|
|
|
1174 # Positionm3<-which(goodones[,5] %in% TRUE)
|
|
|
1175 # if (length(Positionm3)<2){Positionm3<-bareSDs[,5][order(bareSDs[,5])[1:2]]}
|
|
|
1176 # Positionm2<-which(goodones[,6] %in% TRUE)
|
|
|
1177 # if (length(Positionm2)<2){Positionm2<-bareSDs[,6][order(bareSDs[,6])[1:2]]}
|
|
|
1178 # Positionm1<-which(goodones[,7] %in% TRUE)
|
|
|
1179 # if (length(Positionm1)<2){Positionm1<-bareSDs[,7][order(bareSDs[,7])[1:2]]}
|
|
|
1180 #
|
|
|
1181 # Positiond0<-which(goodones[,8] %in% TRUE)
|
|
|
1182 # if (length(Positiond0)<1){Positiond0<-which(bareSDs[,8]==max(bareSDs[,8]))}
|
|
|
1183 #
|
|
|
1184 # Positionp1<-which(goodones[,9] %in% TRUE)
|
|
|
1185 # if (length(Positionp1)<2){Positionp1<-bareSDs[,9][order(bareSDs[,9])[1:2]]}
|
|
|
1186 # Positionp2<-which(goodones[,10] %in% TRUE)
|
|
|
1187 # if (length(Positionp2)<2){Positionp2<-bareSDs[,10][order(bareSDs[,10])[1:2]]}
|
|
|
1188 # Positionp3<-which(goodones[,11] %in% TRUE)
|
|
|
1189 # if (length(Positionp3)<2){Positionp3<-bareSDs[,11][order(bareSDs[,11])[1:2]]}
|
|
|
1190 # Positionp4<-which(goodones[,12] %in% TRUE)
|
|
|
1191 # if (length(Positionp4)<2){Positionp4<-bareSDs[,12][order(bareSDs[,12])[1:2]]}
|
|
|
1192 # Positionp5<-which(goodones[,13] %in% TRUE)
|
|
|
1193 # if (length(Positionp5)<1){Positionp5<-which(bareSDs[,13]==max(bareSDs[,13]))}
|
|
|
1194 # Positionp6<-which(goodones[,14] %in% TRUE)
|
|
|
1195 # if (length(Positionp6)<1){Positionp6<-which(bareSDs[,14]==max(bareSDs[,14]))}
|
|
|
1196 # Positionp7<-which(goodones[,15] %in% TRUE)
|
|
|
1197 # if (length(Positionp7)<1){Positionp7<-which(bareSDs[,15]==max(bareSDs[,15]))}
|
|
|
1198
|
|
|
1199
|
|
|
1200
|
|
|
1201
|
|
|
1202 # Positionm7<-which(goodones[,1] %in% TRUE)
|
|
|
1203 # if (length(Positionm7)<1){Positionm7<-which(bareSDs[,1]==max(bareSDs[,1]))}
|
|
|
1204 # Positionm6<-which(goodones[,2] %in% TRUE)
|
|
|
1205 # if (length(Positionm6)<1){Positionm6<-which(bareSDs[,2]==max(bareSDs[,2]))}
|
|
|
1206 # Positionm5<-which(goodones[,3] %in% TRUE)
|
|
|
1207 # if (length(Positionm5)<1){Positionm5<-which(bareSDs[,3]==max(bareSDs[,3]))}
|
|
|
1208 # Positionm4<-which(goodones[,4] %in% TRUE)
|
|
|
1209 # if (length(Positionm4)<1){Positionm4<-which(bareSDs[,4]==max(bareSDs[,4]))}
|
|
|
1210 # Positionm3<-which(goodones[,5] %in% TRUE)
|
|
|
1211 # if (length(Positionm3)<1){Positionm3<-which(bareSDs[,5]==max(bareSDs[,5]))}
|
|
|
1212 # Positionm2<-which(goodones[,6] %in% TRUE)
|
|
|
1213 # if (length(Positionm2)<1){Positionm2<-which(bareSDs[,6]==max(bareSDs[,6]))}
|
|
|
1214 # Positionm1<-which(goodones[,7] %in% TRUE)
|
|
|
1215 # if (length(Positionm1)<1){Positionm1<-which(bareSDs[,7]==max(bareSDs[,7]))}
|
|
|
1216 #
|
|
|
1217 # Positiond0<-which(goodones[,8] %in% TRUE)
|
|
|
1218 # if (length(Positiond0)<1){Positiond0<-which(bareSDs[,8]==max(bareSDs[,8]))}
|
|
|
1219 #
|
|
|
1220 # Positionp1<-which(goodones[,9] %in% TRUE)
|
|
|
1221 # if (length(Positionp1)<1){Positionp1<-which(bareSDs[,9]==max(bareSDs[,9]))}
|
|
|
1222 # Positionp2<-which(goodones[,10] %in% TRUE)
|
|
|
1223 # if (length(Positionp2)<1){Positionp2<-which(bareSDs[,10]==max(bareSDs[,10]))}
|
|
|
1224 # Positionp3<-which(goodones[,11] %in% TRUE)
|
|
|
1225 # if (length(Positionp3)<1){Positionp3<-which(bareSDs[,11]==max(bareSDs[,11]))}
|
|
|
1226 # Positionp4<-which(goodones[,12] %in% TRUE)
|
|
|
1227 # if (length(Positionp4)<1){Positionp4<-which(bareSDs[,12]==max(bareSDs[,12]))}
|
|
|
1228 # Positionp5<-which(goodones[,13] %in% TRUE)
|
|
|
1229 # if (length(Positionp5)<1){Positionp5<-which(bareSDs[,13]==max(bareSDs[,13]))}
|
|
|
1230 # Positionp6<-which(goodones[,14] %in% TRUE)
|
|
|
1231 # if (length(Positionp6)<1){Positionp6<-which(bareSDs[,14]==max(bareSDs[,14]))}
|
|
|
1232 # Positionp7<-which(goodones[,15] %in% TRUE)
|
|
|
1233 # if (length(Positionp7)<1){Positionp7<-which(bareSDs[,15]==max(bareSDs[,15]))}
|
|
|
1234
|
|
|
1235 match(c(bareSDs[,2][order(bareSDs[,2])[1:2]]),bareSDs[,2])
|
|
|
1236
|
|
|
1237 Positionm7<-which(goodones[,1] %in% TRUE)
|
|
|
1238 if (length(Positionm7)<3){Positionm7<-match(c(bareSDs[,1][order(bareSDs[,1])[19:20]]),bareSDs[,1])}
|
|
|
1239 Positionm6<-which(goodones[,2] %in% TRUE)
|
|
|
1240 if (length(Positionm6)<3){Positionm6<-match(c(bareSDs[,2][order(bareSDs[,2])[19:20]]),bareSDs[,2])}
|
|
|
1241 Positionm5<-which(goodones[,3] %in% TRUE)
|
|
|
1242 if (length(Positionm5)<3){Positionm5<-match(c(bareSDs[,3][order(bareSDs[,3])[19:20]]),bareSDs[,3])}
|
|
|
1243 Positionm4<-which(goodones[,4] %in% TRUE)
|
|
|
1244 if (length(Positionm4)<3){Positionm4<-match(c(bareSDs[,4][order(bareSDs[,4])[19:20]]),bareSDs[,4])}
|
|
|
1245 Positionm3<-which(goodones[,5] %in% TRUE)
|
|
|
1246 if (length(Positionm3)<3){Positionm3<-match(c(bareSDs[,5][order(bareSDs[,5])[19:20]]),bareSDs[,5])}
|
|
|
1247 Positionm2<-which(goodones[,6] %in% TRUE)
|
|
|
1248 if (length(Positionm2)<3){Positionm2<-match(c(bareSDs[,6][order(bareSDs[,6])[19:20]]),bareSDs[,6])}
|
|
|
1249 Positionm1<-which(goodones[,7] %in% TRUE)
|
|
|
1250 if (length(Positionm1)<3){Positionm1<-match(c(bareSDs[,7][order(bareSDs[,7])[19:20]]),bareSDs[,7])}
|
|
|
1251
|
|
|
1252 Positiond0<-which(goodones[,8] %in% TRUE)
|
|
|
1253 #if (length(Positiond0)<3){Positiond0<-bareSDs[,8][order(bareSDs[,8])[1:2]]}
|
|
|
1254
|
|
|
1255 Positionp1<-which(goodones[,9] %in% TRUE)
|
|
|
1256 if (length(Positionp1)<3){Positionp1<-match(c(bareSDs[,9][order(bareSDs[,9])[19:20]]),bareSDs[,9])}
|
|
|
1257 Positionp2<-which(goodones[,10] %in% TRUE)
|
|
|
1258 if (length(Positionp2)<3){Positionp2<-match(c(bareSDs[,10][order(bareSDs[,10])[19:20]]),bareSDs[,10])}
|
|
|
1259 Positionp3<-which(goodones[,11] %in% TRUE)
|
|
|
1260 if (length(Positionp3)<3){Positionp3<-match(c(bareSDs[,11][order(bareSDs[,11])[19:20]]),bareSDs[,11])}
|
|
|
1261 Positionp4<-which(goodones[,12] %in% TRUE)
|
|
|
1262 if (length(Positionp4)<3){Positionp4<-match(c(bareSDs[,12][order(bareSDs[,12])[19:20]]),bareSDs[,12])}
|
|
|
1263 Positionp5<-which(goodones[,13] %in% TRUE)
|
|
|
1264 if (length(Positionp5)<3){Positionp5<-match(c(bareSDs[,13][order(bareSDs[,13])[19:20]]),bareSDs[,13])}
|
|
|
1265 Positionp6<-which(goodones[,14] %in% TRUE)
|
|
|
1266 if (length(Positionp6)<3){Positionp6<-match(c(bareSDs[,14][order(bareSDs[,14])[19:20]]),bareSDs[,14])}
|
|
|
1267 Positionp7<-which(goodones[,15] %in% TRUE)
|
|
|
1268 if (length(Positionp7)<3){Positionp7<-match(c(bareSDs[,15][order(bareSDs[,15])[19:20]]),bareSDs[,15])}
|
|
|
1269
|
|
|
1270
|
|
|
1271 aa_props2 <- c("1"="A", "2"="C", "3"="D", "4"="E", "5"="F", "6"="G", "7"="H", "8"="I", "9"="K", "10"="L", "11"="M", "12"="N",
|
|
|
1272 "13"="P", "14"="Q", "15"="R", "16"="S", "17"="T", "18"="V", "19"="W", "20"="Y")
|
|
|
1273
|
|
|
1274 Positionm7<-sapply(Positionm7, function (x) aa_props2[x])
|
|
|
1275 Positionm6<-sapply(Positionm6, function (x) aa_props2[x])
|
|
|
1276 Positionm5<-sapply(Positionm5, function (x) aa_props2[x])
|
|
|
1277 Positionm4<-sapply(Positionm4, function (x) aa_props2[x])
|
|
|
1278 Positionm3<-sapply(Positionm3, function (x) aa_props2[x])
|
|
|
1279 Positionm2<-sapply(Positionm2, function (x) aa_props2[x])
|
|
|
1280 Positionm1<-sapply(Positionm1, function (x) aa_props2[x])
|
|
|
1281 Positiond0<-sapply(Positiond0, function (x) aa_props2[x])
|
|
|
1282 Positionp1<-sapply(Positionp1, function (x) aa_props2[x])
|
|
|
1283 Positionp2<-sapply(Positionp2, function (x) aa_props2[x])
|
|
|
1284 Positionp3<-sapply(Positionp3, function (x) aa_props2[x])
|
|
|
1285 Positionp4<-sapply(Positionp4, function (x) aa_props2[x])
|
|
|
1286 Positionp5<-sapply(Positionp5, function (x) aa_props2[x])
|
|
|
1287 Positionp6<-sapply(Positionp6, function (x) aa_props2[x])
|
|
|
1288 Positionp7<-sapply(Positionp7, function (x) aa_props2[x])
|
|
|
1289
|
|
|
1290
|
|
|
1291 # Positionm7<-c("D","H","N","V")
|
|
|
1292 # Positionm6<-c("E","V")
|
|
|
1293 # Positionm5<-c("D","H")
|
|
|
1294 # Positionm4<-c("D","N")
|
|
|
1295 # Positionm3<-c("D","E","F","Q")
|
|
|
1296 # Positionm2<-c("D","N","Q","S")
|
|
|
1297 # Positionm1<-c("F","I","L")
|
|
|
1298 # Positiond0<-c("Y")
|
|
|
1299 # Positionp1<-c("A","E")
|
|
|
1300 # Positionp2<-c("T","S","Q","E")
|
|
|
1301 # Positionp3<-c("V")
|
|
|
1302 # Positionp4<-c("K")
|
|
|
1303 # Positionp5<-c("K")
|
|
|
1304 # Positionp6<-c("K")
|
|
|
1305 # Positionp7<-c("R")
|
|
|
1306 #this is where the amino acids for each position are given. m means minus, p mean plus
|
|
|
1307 ########################################
|
|
|
1308 # ScreenerFilename<-"C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls"
|
|
|
1309
|
|
|
1310
|
|
|
1311
|
|
|
1312
|
|
|
1313
|
|
|
1314
|
|
|
1315
|
|
|
1316
|
|
|
1317
|
|
|
1318
|
|
|
1319
|
|
|
1320 screaner<-read.csv(ScreenerFilename, header = FALSE, stringsAsFactors = FALSE)
|
|
|
1321
|
|
|
1322
|
|
|
1323 AKT<-screaner[2:25,]
|
|
|
1324 AMPK<-screaner[27:50,]
|
|
|
1325 CDK1<-screaner[52:75,]
|
|
|
1326 CHK1<-screaner[77:100,]
|
|
|
1327 CK2A1<-screaner[102:125,]
|
|
|
1328 LKB1<-screaner[127:150,]
|
|
|
1329 MAPK3<-screaner[152:175,]
|
|
|
1330 MAPK13<-screaner[177:200,]
|
|
|
1331 MTOR<-screaner[202:225,]
|
|
|
1332 # Pyk2<-screaner[227:250,]
|
|
|
1333 # Src<-screaner[252:275,]
|
|
|
1334 # Syk<-screaner[277:300,]
|
|
|
1335 # Yes<-screaner[302:325,]
|
|
|
1336
|
|
|
1337 #two questions: why are we doing CDK1 when we already have a bioninformatics page about it?
|
|
|
1338 #two I reran everything and only get 96 positions of interest in the SD table
|
|
|
1339
|
|
|
1340
|
|
|
1341
|
|
|
1342
|
|
|
1343
|
|
|
1344
|
|
|
1345
|
|
|
1346
|
|
|
1347
|
|
|
1348 #Do_You_want_An_Excel_Output_Questionmark<-"NO"
|
|
|
1349 GeneratedPeptidesFile<-"GeneratedPeptidesFile.csv"
|
|
|
1350
|
|
|
1351
|
|
|
1352 # AKT<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 4)
|
|
|
1353 # AMPK<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 5)
|
|
|
1354 # CDK1<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 6)
|
|
|
1355 # CHK1<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 7)
|
|
|
1356 # CK2A1<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 8)
|
|
|
1357 # LKB1<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 9)
|
|
|
1358 # MAPK3<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 10)
|
|
|
1359 # MAPK13<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 11)
|
|
|
1360 # MTOR<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 12)
|
|
|
1361 # Pyk2<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 13)
|
|
|
1362 # Src<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 14)
|
|
|
1363 # Syk<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 15)
|
|
|
1364 # Yes<-read.xlsx("C:/Users/User Name/Desktop/UMN 2017 Spring/Parker Lab/Kinatest ID/Screener.xls", sheetIndex = 16)
|
|
|
1365 #
|
|
|
1366
|
|
|
1367
|
|
|
1368 "A"=1
|
|
|
1369 "C"=2
|
|
|
1370 "D"=3
|
|
|
1371 "E"=4
|
|
|
1372 "F"=5
|
|
|
1373 "G"=6
|
|
|
1374 "H"=7
|
|
|
1375 "I"=8
|
|
|
1376 "K"=9
|
|
|
1377 "L"=10
|
|
|
1378 "M"=11
|
|
|
1379 "N"=12
|
|
|
1380 "P"=13
|
|
|
1381 "Q"=14
|
|
|
1382 "R"=15
|
|
|
1383 "S"=16
|
|
|
1384 "T"=17
|
|
|
1385 "V"=18
|
|
|
1386 "W"=19
|
|
|
1387 "Y"=20
|
|
|
1388
|
|
|
1389 aa_props <- c("A"=A, "C"=C, "D"=D, "E"=E, "F"=F,"G"=G,"H"=H,"I"=I,"K"=K,"L"=L,"M"=M,"N"=N,"P"=P,"Q"=Q,"R"=R,
|
|
|
1390 "S"=S,"T"=T,"V"=V,"W"=W,"Y"=Y,"xY"=Y,"O"=21)
|
|
|
1391
|
|
|
1392 number15<-sapply(Positionm7, function (x) aa_props[x])
|
|
|
1393 number14<-sapply(Positionm6, function (x) aa_props[x])
|
|
|
1394 number13<-sapply(Positionm5, function (x) aa_props[x])
|
|
|
1395 number1 <- sapply(Positionm4, function (x) aa_props[x])
|
|
|
1396 number2 <- sapply(Positionm3, function (x) aa_props[x])
|
|
|
1397 number3 <- sapply(Positionm2, function (x) aa_props[x])
|
|
|
1398 number4 <- sapply(Positionm1, function (x) aa_props[x])
|
|
|
1399 number5 <- sapply(Positiond0, function (x) aa_props[x])
|
|
|
1400 number6 <- sapply(Positionp1, function (x) aa_props[x])
|
|
|
1401 number7 <- sapply(Positionp2, function (x) aa_props[x])
|
|
|
1402 number8 <- sapply(Positionp3, function (x) aa_props[x])
|
|
|
1403 number9 <- sapply(Positionp4, function (x) aa_props[x])
|
|
|
1404 number10<-sapply(Positionp5, function (x) aa_props[x])
|
|
|
1405 number11<-sapply(Positionp6, function (x) aa_props[x])
|
|
|
1406 number12<-sapply(Positionp7, function (x) aa_props[x])
|
|
|
1407
|
|
|
1408 # number1<-Positionm4
|
|
|
1409 # number2<-Positionm3
|
|
|
1410 # number3<-Positionm2
|
|
|
1411 # number4<-Positionm1
|
|
|
1412 # number5<-Positiond0
|
|
|
1413 # number6<-Positionp1
|
|
|
1414 # number7<-Positionp2
|
|
|
1415 # number8<-Positionp3
|
|
|
1416 # number9<-Positionp4
|
|
|
1417
|
|
|
1418 #############################
|
|
|
1419 ########################################
|
|
|
1420
|
|
|
1421
|
|
|
1422 total=length(Positionp7)*length(Positionp6)*length(Positionp5)*length(Positionp4)*length(Positionp3)*(length(Positionp2))*length(Positionp1)*
|
|
|
1423 length(Positiond0)*length(Positionm1)*length(Positionm2)*length(Positionm3)*length(Positionm4)*length(Positionm5)*length(Positionm6)*length(Positionm7)
|
|
|
1424 #this is just a way to doublecheck that the length of the generated peptides vector is correct
|
|
|
1425
|
|
|
1426 GeneratedPeptides<-rep(NA, times=total*15)
|
|
|
1427 GeneratedPeptides<-matrix(data = GeneratedPeptides,ncol = 15)
|
|
|
1428
|
|
|
1429 NumeratedPeptides<-GeneratedPeptides
|
|
|
1430 #create an empty vector of correct length by finding the number of each AAs per position and multiplying them
|
|
|
1431 count<-0
|
|
|
1432 for (t in 1:length(Positionm7)) {
|
|
|
1433 for (s in 1:length(Positionm6)) {
|
|
|
1434 for (r in 1:length(Positionm5)) {
|
|
|
1435 for (i in 1:length(Positionm4)) {
|
|
|
1436 for (j in 1:length(Positionm3)) {
|
|
|
1437 for (k in 1:length(Positionm2)) {
|
|
|
1438 for (l in 1:length(Positionm1)) {
|
|
|
1439 for (m in 1:length(Positiond0)) {
|
|
|
1440 for (n in 1:length(Positionp1)) {
|
|
|
1441 for (o in 1:length(Positionp2)) {
|
|
|
1442 for (p in 1:length(Positionp3)) {
|
|
|
1443 for (q in 1:length(Positionp4)) {
|
|
|
1444 for (u in 1:length(Positionp5)) {
|
|
|
1445 for (v in 1:length(Positionp6)) {
|
|
|
1446 for (w in 1:length(Positionp7)) {
|
|
|
1447 # i=1
|
|
|
1448 # j=1
|
|
|
1449 # k=1
|
|
|
1450 # l=1
|
|
|
1451 # m=1
|
|
|
1452 # n=1
|
|
|
1453 # o=1
|
|
|
1454 # p=1
|
|
|
1455 # q=1
|
|
|
1456 #
|
|
|
1457 #for every single position, increment the count number, create a peptide using the AAs at that position
|
|
|
1458 #then put them together into the generated peptides sequencex
|
|
|
1459 count<-count+1
|
|
|
1460 tabulation<-c(Positionm7[t],Positionm6[s],Positionm5[r],Positionm4[i],Positionm3[j],Positionm2[k],Positionm1[l],Positiond0[m],Positionp1[n],
|
|
|
1461 Positionp2[o],Positionp3[p],Positionp4[q],Positionp5[u],Positionp6[v],Positionp7[w])
|
|
|
1462 numeration<-c(number15[t],number14[s],number13[r],number1[i],number2[j],number3[k],number4[l],number5[m],number6[n],number7[o],number8[p],number9[q],number10[u],number11[v],
|
|
|
1463 number12[w])
|
|
|
1464 #tabulation<-paste(tabulation, sep="", collapse="")
|
|
|
1465 GeneratedPeptides[count,1:15]<-tabulation
|
|
|
1466 NumeratedPeptides[count,1:15]<-numeration
|
|
|
1467 }
|
|
|
1468 }
|
|
|
1469 }
|
|
|
1470 }
|
|
|
1471 }
|
|
|
1472 }
|
|
|
1473 }
|
|
|
1474 }
|
|
|
1475 }
|
|
|
1476 }
|
|
|
1477 }
|
|
|
1478 }
|
|
|
1479 }
|
|
|
1480 }
|
|
|
1481 }
|
|
|
1482 ####################################################################
|
|
|
1483 #now here I use the Endogenous Probabilty matrix from the previous script, which is called EMPtable
|
|
|
1484 #to score the created peptides
|
|
|
1485 ThisKinTable<-EPMtableu#[1:nrow(SDtable),]
|
|
|
1486 TKTcolumn<-c(data=rep(1,times=21))
|
|
|
1487 TKTcolumn<-as.matrix(TKTcolumn,ncol=1)
|
|
|
1488 ThisKinTable<-cbind(TKTcolumn,ThisKinTable)
|
|
|
1489
|
|
|
1490 ThisKinGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
|
|
|
1491 ThisKinGenWeirdScore<-rep(NA,times=nrow(GeneratedPeptides))
|
|
|
1492
|
|
|
1493 for (x in 1:nrow(GeneratedPeptides)){
|
|
|
1494 Scoringpeptide<-NumeratedPeptides[x,1:15]
|
|
|
1495 Scoringpeptide<-Scoringpeptide+1
|
|
|
1496 ThisKinTableScore<-as.numeric(ThisKinTable[Scoringpeptide[1],3])*ThisKinTable[as.numeric(Scoringpeptide[2]),4]*ThisKinTable[as.numeric(Scoringpeptide[3]),5]*
|
|
|
1497 ThisKinTable[as.numeric(Scoringpeptide[4]),6]*ThisKinTable[as.numeric(Scoringpeptide[5]),7]*ThisKinTable[as.numeric(Scoringpeptide[6]),8]*ThisKinTable[as.numeric(Scoringpeptide[7]),9]*
|
|
|
1498 #ThisKinTable[as.numeric(Scoringpeptide[8]),10]*
|
|
|
1499 ThisKinTable[as.numeric(Scoringpeptide[9]),11]*ThisKinTable[as.numeric(Scoringpeptide[10]),12]*ThisKinTable[as.numeric(Scoringpeptide[11]),13]*
|
|
|
1500 ThisKinTable[as.numeric(Scoringpeptide[12]),14]*ThisKinTable[as.numeric(Scoringpeptide[13]),15]*ThisKinTable[as.numeric(Scoringpeptide[14]),16]*ThisKinTable[as.numeric(Scoringpeptide[15]),17]
|
|
|
1501 ThisKinGeneratedScores[x]<-ThisKinTableScore
|
|
|
1502 ThisKinTableScore<-(ThisKinTableScore/(ThisKinTableScore+1/as.numeric(NormalizationScore[2])))
|
|
|
1503 ThisKinGenWeirdScore[x]<-ThisKinTableScore
|
|
|
1504 }
|
|
|
1505
|
|
|
1506 AKTGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
|
|
|
1507 AMPKGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
|
|
|
1508 CDK1GeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
|
|
|
1509 CHK1GeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
|
|
|
1510 CK2A1GeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
|
|
|
1511 LKB1GeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
|
|
|
1512 MAPK3GeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
|
|
|
1513 MAPK13GeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
|
|
|
1514 MTORGeneratedScores<-rep(NA,times=nrow(GeneratedPeptides))
|
|
|
1515
|
|
|
1516 for (x in 1:nrow(GeneratedPeptides)){
|
|
|
1517 Scoringpeptide<-NumeratedPeptides[x,1:15]
|
|
|
1518 AKTScore<-AKT[Scoringpeptide[1],2]*AKT[Scoringpeptide[2],3]*AKT[Scoringpeptide[3],4]*AKT[Scoringpeptide[4],5]*AKT[Scoringpeptide[5],6]*AKT[Scoringpeptide[6],7]*
|
|
|
1519 AKT[Scoringpeptide[7],8]*AKT[Scoringpeptide[9],10]*AKT[Scoringpeptide[10],11]*AKT[Scoringpeptide[11],12]*AKT[Scoringpeptide[12],13]*
|
|
|
1520 AKT[Scoringpeptide[13],14]*AKT[Scoringpeptide[14],15]*AKT[Scoringpeptide[15],16]
|
|
|
1521 AKTGeneratedScores[x]<-AKTScore
|
|
|
1522
|
|
|
1523 AMPKScore<-AMPK[Scoringpeptide[1],2]*AMPK[Scoringpeptide[2],3]*AMPK[Scoringpeptide[3],4]*AMPK[Scoringpeptide[4],5]*AMPK[Scoringpeptide[5],6]*AMPK[Scoringpeptide[6],7]*
|
|
|
1524 AMPK[Scoringpeptide[7],8]*AMPK[Scoringpeptide[9],10]*AMPK[Scoringpeptide[10],11]*AMPK[Scoringpeptide[11],12]*AMPK[Scoringpeptide[12],13]*
|
|
|
1525 AMPK[Scoringpeptide[13],14]*AMPK[Scoringpeptide[14],15]*AMPK[Scoringpeptide[15],16]
|
|
|
1526 AMPKGeneratedScores[x]<-AMPKScore
|
|
|
1527
|
|
|
1528 CDK1Score<-CDK1[Scoringpeptide[1],2]*CDK1[Scoringpeptide[2],3]*CDK1[Scoringpeptide[3],4]*CDK1[Scoringpeptide[4],5]*CDK1[Scoringpeptide[5],6]*CDK1[Scoringpeptide[6],7]*
|
|
|
1529 CDK1[Scoringpeptide[7],8]*CDK1[Scoringpeptide[9],10]*CDK1[Scoringpeptide[10],11]*CDK1[Scoringpeptide[11],12]*CDK1[Scoringpeptide[12],13]*
|
|
|
1530 CDK1[Scoringpeptide[13],14]*CDK1[Scoringpeptide[14],15]*CDK1[Scoringpeptide[15],16]
|
|
|
1531 CDK1GeneratedScores[x]<-CDK1Score
|
|
|
1532
|
|
|
1533 CHK1Score<-CHK1[Scoringpeptide[1],2]*CHK1[Scoringpeptide[2],3]*CHK1[Scoringpeptide[3],4]*CHK1[Scoringpeptide[4],5]*CHK1[Scoringpeptide[5],6]*CHK1[Scoringpeptide[6],7]*
|
|
|
1534 CHK1[Scoringpeptide[7],8]*CHK1[Scoringpeptide[9],10]*CHK1[Scoringpeptide[10],11]*CHK1[Scoringpeptide[11],12]*CHK1[Scoringpeptide[12],13]*
|
|
|
1535 CHK1[Scoringpeptide[13],14]*CHK1[Scoringpeptide[14],15]*CHK1[Scoringpeptide[15],16]
|
|
|
1536 CHK1GeneratedScores[x]<-CHK1Score
|
|
|
1537
|
|
|
1538 CK2A1Score<-CK2A1[Scoringpeptide[1],2]*CK2A1[Scoringpeptide[2],3]*CK2A1[Scoringpeptide[3],4]*CK2A1[Scoringpeptide[4],5]*CK2A1[Scoringpeptide[5],6]*CK2A1[Scoringpeptide[6],7]*
|
|
|
1539 CK2A1[Scoringpeptide[7],8]*CK2A1[Scoringpeptide[9],10]*CK2A1[Scoringpeptide[10],11]*CK2A1[Scoringpeptide[11],12]*CK2A1[Scoringpeptide[12],13]*
|
|
|
1540 CK2A1[Scoringpeptide[13],14]*CK2A1[Scoringpeptide[14],15]*CK2A1[Scoringpeptide[15],16]
|
|
|
1541 CK2A1GeneratedScores[x]<-CK2A1Score
|
|
|
1542
|
|
|
1543 LKB1Score<-LKB1[Scoringpeptide[1],2]*LKB1[Scoringpeptide[2],3]*LKB1[Scoringpeptide[3],4]*LKB1[Scoringpeptide[4],5]*LKB1[Scoringpeptide[5],6]*LKB1[Scoringpeptide[6],7]*
|
|
|
1544 LKB1[Scoringpeptide[7],8]*LKB1[Scoringpeptide[9],10]*LKB1[Scoringpeptide[10],11]*LKB1[Scoringpeptide[11],12]*LKB1[Scoringpeptide[12],13]*
|
|
|
1545 LKB1[Scoringpeptide[13],14]*LKB1[Scoringpeptide[14],15]*LKB1[Scoringpeptide[15],16]
|
|
|
1546 LKB1GeneratedScores[x]<-LKB1Score
|
|
|
1547
|
|
|
1548 MAPK3Score<-MAPK3[Scoringpeptide[1],2]*MAPK3[Scoringpeptide[2],3]*MAPK3[Scoringpeptide[3],4]*MAPK3[Scoringpeptide[4],5]*MAPK3[Scoringpeptide[5],6]*MAPK3[Scoringpeptide[6],7]*
|
|
|
1549 MAPK3[Scoringpeptide[7],8]*MAPK3[Scoringpeptide[9],10]*MAPK3[Scoringpeptide[10],11]*MAPK3[Scoringpeptide[11],12]*MAPK3[Scoringpeptide[12],13]*
|
|
|
1550 MAPK3[Scoringpeptide[13],14]*MAPK3[Scoringpeptide[14],15]*MAPK3[Scoringpeptide[15],16]
|
|
|
1551 MAPK3GeneratedScores[x]<-MAPK3Score
|
|
|
1552
|
|
|
1553 MAPK13Score<-MAPK13[Scoringpeptide[1],2]*MAPK13[Scoringpeptide[2],3]*MAPK13[Scoringpeptide[3],4]*MAPK13[Scoringpeptide[4],5]*MAPK13[Scoringpeptide[5],6]*MAPK13[Scoringpeptide[6],7]*
|
|
|
1554 MAPK13[Scoringpeptide[7],8]*MAPK13[Scoringpeptide[9],10]*MAPK13[Scoringpeptide[10],11]*MAPK13[Scoringpeptide[11],12]*MAPK13[Scoringpeptide[12],13]*
|
|
|
1555 MAPK13[Scoringpeptide[13],14]*MAPK13[Scoringpeptide[14],15]*MAPK13[Scoringpeptide[15],16]
|
|
|
1556 MAPK13GeneratedScores[x]<-MAPK13Score
|
|
|
1557
|
|
|
1558 MTORScore<-MTOR[Scoringpeptide[1],2]*MTOR[Scoringpeptide[2],3]*MTOR[Scoringpeptide[3],4]*MTOR[Scoringpeptide[4],5]*MTOR[Scoringpeptide[5],6]*MTOR[Scoringpeptide[6],7]*
|
|
|
1559 MTOR[Scoringpeptide[7],8]*MTOR[Scoringpeptide[9],10]*MTOR[Scoringpeptide[10],11]*MTOR[Scoringpeptide[11],12]*MTOR[Scoringpeptide[12],13]*
|
|
|
1560 MTOR[Scoringpeptide[13],14]*MTOR[Scoringpeptide[14],15]*MTOR[Scoringpeptide[15],16]
|
|
|
1561 MTORGeneratedScores[x]<-MTORScore
|
|
|
1562
|
|
|
1563 # Pyk2Score<-Pyk2[Scoringpeptide[1],2]*Pyk2[Scoringpeptide[2],3]*Pyk2[Scoringpeptide[3],4]*Pyk2[Scoringpeptide[4],5]*Pyk2[Scoringpeptide[5],6]*Pyk2[Scoringpeptide[6],7]*
|
|
|
1564 # Pyk2[Scoringpeptide[7],8]*Pyk2[Scoringpeptide[9],10]*Pyk2[Scoringpeptide[10],11]*Pyk2[Scoringpeptide[11],12]*Pyk2[Scoringpeptide[12],13]*
|
|
|
1565 # Pyk2[Scoringpeptide[13],14]*Pyk2[Scoringpeptide[14],15]*Pyk2[Scoringpeptide[15],16]
|
|
|
1566 # Pyk2GeneratedScores[x]<-Pyk2Score
|
|
|
1567 #
|
|
|
1568 # SrcScore<-Src[Scoringpeptide[1],2]*Src[Scoringpeptide[2],3]*Src[Scoringpeptide[3],4]*Src[Scoringpeptide[4],5]*Src[Scoringpeptide[5],6]*Src[Scoringpeptide[6],7]*
|
|
|
1569 # Src[Scoringpeptide[7],8]*Src[Scoringpeptide[9],10]*Src[Scoringpeptide[10],11]*Src[Scoringpeptide[11],12]*Src[Scoringpeptide[12],13]*
|
|
|
1570 # Src[Scoringpeptide[13],14]*Src[Scoringpeptide[14],15]*Src[Scoringpeptide[15],16]
|
|
|
1571 # SrcGeneratedScores[x]<-SrcScore
|
|
|
1572 #
|
|
|
1573 # SykScore<-Syk[Scoringpeptide[1],2]*Syk[Scoringpeptide[2],3]*Syk[Scoringpeptide[3],4]*Syk[Scoringpeptide[4],5]*Syk[Scoringpeptide[5],6]*Syk[Scoringpeptide[6],7]*
|
|
|
1574 # Syk[Scoringpeptide[7],8]*Syk[Scoringpeptide[9],10]*Syk[Scoringpeptide[10],11]*Syk[Scoringpeptide[11],12]*Syk[Scoringpeptide[12],13]*
|
|
|
1575 # Syk[Scoringpeptide[13],14]*Syk[Scoringpeptide[14],15]*Syk[Scoringpeptide[15],16]
|
|
|
1576 # SykGeneratedScores[x]<-SykScore
|
|
|
1577 #
|
|
|
1578 # YesScore<-Yes[Scoringpeptide[1],2]*Yes[Scoringpeptide[2],3]*Yes[Scoringpeptide[3],4]*Yes[Scoringpeptide[4],5]*Yes[Scoringpeptide[5],6]*Yes[Scoringpeptide[6],7]*
|
|
|
1579 # Yes[Scoringpeptide[7],8]*Yes[Scoringpeptide[9],10]*Yes[Scoringpeptide[10],11]*Yes[Scoringpeptide[11],12]*Yes[Scoringpeptide[12],13]*
|
|
|
1580 # Yes[Scoringpeptide[13],14]*Yes[Scoringpeptide[14],15]*Yes[Scoringpeptide[15],16]
|
|
|
1581 # YesGeneratedScores[x]<-YesScore
|
|
|
1582
|
|
|
1583 # ThisKinTableScore<-ThisKinTable[as.numeric(Scoringpeptide[1]),3]*ThisKinTable[as.numeric(Scoringpeptide[2]),4]*ThisKinTable[as.numeric(Scoringpeptide[3]),5]*
|
|
|
1584 # ThisKinTable[as.numeric(Scoringpeptide[4]),6]*ThisKinTable[as.numeric(Scoringpeptide[6]),8]*
|
|
|
1585 # ThisKinTable[as.numeric(Scoringpeptide[7]),9]*ThisKinTable[as.numeric(Scoringpeptide[8]),10]*ThisKinTable[as.numeric(Scoringpeptide[9]),11]
|
|
|
1586 # ThisKinGeneratedScores[x]<-ThisKinTableScore
|
|
|
1587 }
|
|
|
1588
|
|
|
1589
|
|
|
1590
|
|
|
1591 AKTNorm<-1/as.numeric(AKT[22,1])
|
|
|
1592 AKTThresh<-as.numeric(AKT[24,1])
|
|
|
1593 AKTTrueThresh<-((AKTThresh*AKTNorm)/(100-AKTThresh))
|
|
|
1594 AKTActive<-unlist(AKTGeneratedScores)>AKTTrueThresh
|
|
|
1595 if (TodaysKinase=="AKT"){AKTActive<-rep(0,times=nrow(GeneratedPeptides))}
|
|
|
1596
|
|
|
1597 AMPKNorm<-1/as.numeric(AMPK[22,1])
|
|
|
1598 AMPKThresh<-as.numeric(AMPK[24,1])
|
|
|
1599 AMPKTrueThresh<-((AMPKThresh*AMPKNorm)/(100-AMPKThresh))
|
|
|
1600 AMPKActive<-unlist(AMPKGeneratedScores)>AMPKTrueThresh
|
|
|
1601 if (TodaysKinase=="AMPK"){AMPKActive<-rep(0,times=nrow(GeneratedPeptides))}
|
|
|
1602
|
|
|
1603 CDK1Norm<-1/as.numeric(CDK1[22,1])
|
|
|
1604 CDK1Thresh<-as.numeric(CDK1[24,1])
|
|
|
1605 CDK1TrueThresh<-((CDK1Thresh*CDK1Norm)/(100-CDK1Thresh))
|
|
|
1606 CDK1Active<-unlist(CDK1GeneratedScores)>CDK1TrueThresh
|
|
|
1607 if (TodaysKinase=="CDK1"){CDK1Active<-rep(0,times=nrow(GeneratedPeptides))}
|
|
|
1608
|
|
|
1609 CHK1Norm<-1/as.numeric(CHK1[22,1])
|
|
|
1610 CHK1Thresh<-as.numeric(CHK1[24,1])
|
|
|
1611 CHK1TrueThresh<-((CHK1Thresh*CHK1Norm)/(100-CHK1Thresh))
|
|
|
1612 CHK1Active<-(CHK1GeneratedScores)>CHK1TrueThresh
|
|
|
1613 if (TodaysKinase=="CHK1"){CHK1Active<-rep(0,times=nrow(GeneratedPeptides))}
|
|
|
1614
|
|
|
1615 CK2A1Norm<-1/as.numeric(CK2A1[22,1])
|
|
|
1616 CK2A1Thresh<-as.numeric(CK2A1[24,1])
|
|
|
1617 CK2A1TrueThresh<-((CK2A1Thresh*CK2A1Norm)/(100-CK2A1Thresh))
|
|
|
1618 CK2A1Active<-unlist(CK2A1GeneratedScores)>CK2A1TrueThresh
|
|
|
1619 if (TodaysKinase=="CK2A1"){CK2A1Active<-rep(0,times=nrow(GeneratedPeptides))}
|
|
|
1620
|
|
|
1621 LKB1Norm<-1/as.numeric(LKB1[22,1])
|
|
|
1622 LKB1Thresh<-as.numeric(LKB1[24,1])
|
|
|
1623 LKB1TrueThresh<-((LKB1Thresh*LKB1Norm)/(100-LKB1Thresh))
|
|
|
1624 LKB1Active<-unlist(LKB1GeneratedScores)>LKB1TrueThresh
|
|
|
1625 if (TodaysKinase=="LKB1"){LKB1Active<-rep(0,times=nrow(GeneratedPeptides))}
|
|
|
1626
|
|
|
1627 MAPK3Norm<-1/as.numeric(MAPK3[22,1])
|
|
|
1628 MAPK3Thresh<-as.numeric(MAPK3[24,1])
|
|
|
1629 MAPK3TrueThresh<-((MAPK3Thresh*MAPK3Norm)/(100-MAPK3Thresh))
|
|
|
1630 MAPK3Active<-unlist(MAPK3GeneratedScores)>MAPK3TrueThresh
|
|
|
1631 if (TodaysKinase=="MAPK3"){MAPK3Active<-rep(0,times=nrow(GeneratedPeptides))}
|
|
|
1632
|
|
|
1633 MAPK13Norm<-1/as.numeric(MAPK13[22,1])
|
|
|
1634 MAPK13Thresh<-as.numeric(MAPK13[24,1])
|
|
|
1635 MAPK13TrueThresh<-((MAPK13Thresh*MAPK13Norm)/(100-MAPK13Thresh))
|
|
|
1636 MAPK13Active<-unlist(MAPK13GeneratedScores)>MAPK13TrueThresh
|
|
|
1637 if (TodaysKinase=="MAPK13"){MAPK13Active<-rep(0,times=nrow(GeneratedPeptides))}
|
|
|
1638
|
|
|
1639 MTORNorm<-1/as.numeric(MTOR[22,1])
|
|
|
1640 MTORThresh<-as.numeric(MTOR[24,1])
|
|
|
1641 MTORTrueThresh<-((MTORThresh*MTORNorm)/(100-MTORThresh))
|
|
|
1642 MTORActive<-unlist(MTORGeneratedScores)>MTORTrueThresh
|
|
|
1643 if (TodaysKinase=="MTOR"){MTORActive<-rep(0,times=nrow(GeneratedPeptides))}
|
|
|
1644
|
|
|
1645 # Pyk2Norm<-1/as.numeric(Pyk2[22,1])
|
|
|
1646 # Pyk2Thresh<-as.numeric(Pyk2[24,1])
|
|
|
1647 # Pyk2TrueThresh<-((Pyk2Thresh*Pyk2Norm)/(100-Pyk2Thresh))
|
|
|
1648 # Pyk2Active<-unlist(Pyk2GeneratedScores)>Pyk2TrueThresh
|
|
|
1649 # if (TodaysKinase=="PYK2"){Pyk2Active<-rep(0,times=nrow(GeneratedPeptides))}
|
|
|
1650 #
|
|
|
1651 # SrcNorm<-1/as.numeric(Src[22,1])
|
|
|
1652 # SrcThresh<-as.numeric(Src[24,1])
|
|
|
1653 # SrcTrueThresh<-((SrcThresh*SrcNorm)/(100-SrcThresh))
|
|
|
1654 # SrcActive<-unlist(SrcGeneratedScores)>SrcTrueThresh
|
|
|
1655 # if (TodaysKinase=="SRC"){SrcActive<-rep(0,times=nrow(GeneratedPeptides))}
|
|
|
1656 #
|
|
|
1657 # SykNorm<-1/as.numeric(Syk[22,1])
|
|
|
1658 # SykThresh<-as.numeric(Syk[24,1])
|
|
|
1659 # SykTrueThresh<-((SykThresh*SykNorm)/(100-SykThresh))
|
|
|
1660 # SykActive<-unlist(SykGeneratedScores)>SykTrueThresh
|
|
|
1661 # if (TodaysKinase=="SYK"){SykActive<-rep(0,times=nrow(GeneratedPeptides))}
|
|
|
1662 #
|
|
|
1663 # YesNorm<-1/as.numeric(Yes[22,1])
|
|
|
1664 # YesThresh<-as.numeric(Yes[24,1])
|
|
|
1665 # YesTrueThresh<-((YesThresh*YesNorm)/(100-YesThresh))
|
|
|
1666 # YesActive<-unlist(YesGeneratedScores)>YesTrueThresh
|
|
|
1667 # if (TodaysKinase=="YES"){YesActive<-rep(0,times=nrow(GeneratedPeptides))}
|
|
|
1668
|
|
|
1669 AllActive<-AKTActive+AMPKActive+CDK1Active+CHK1Active+CK2A1Active+LKB1Active+MAPK3Active+MAPK13Active+MTORActive
|
|
|
1670
|
|
|
1671 Scores<-ThisKinGeneratedScores
|
|
|
1672 ThresholdValues<-ThisKinGenWeirdScore
|
|
|
1673
|
|
|
1674 FullMotifs<-rep("Z",times=nrow(GeneratedPeptides))
|
|
|
1675 for (i in 1:nrow(GeneratedPeptides)) {
|
|
|
1676 motif<-GeneratedPeptides[i,1:15]
|
|
|
1677 motif<-paste(motif,sep = "", collapse = "")
|
|
|
1678 FullMotifs[i]<-motif
|
|
|
1679 }
|
|
|
1680
|
|
|
1681 PeptidesWithRanks<-cbind.data.frame(FullMotifs,GeneratedPeptides,Scores,ThresholdValues)
|
|
|
1682 PeptidesWithRanks<-cbind.data.frame(PeptidesWithRanks,AllActive,AKTActive,AMPKActive,CDK1Active,CHK1Active,CK2A1Active,LKB1Active,MAPK3Active,MAPK13Active,MTORActive)
|
|
|
1683 RanksPeptides<-PeptidesWithRanks[order(PeptidesWithRanks$ThresholdValues,decreasing = FALSE),]
|
|
|
1684 # PepRankHead<-c(1:9,"Sequence","RPMS","PMS")
|
|
|
1685 # RanksPeptides<-rbind.data.frame(PepRankHead,PeptidesWithRanks)
|
|
|
1686 #head(RanksPeptides)
|
|
|
1687
|
|
|
1688
|
|
|
1689 #now I have to score the negative sequences... for some reason
|
|
|
1690 #write up how we transfect with lipofectamine
|
|
|
1691 #3,4,5 questions
|
|
|
1692
|
|
|
1693 #PAUSED EHRE AT 4:50, HOPING THAT FIXING MINERVOTHING SO THAT LEFT SPACES WORKS FIXES A THING. OTHERWISE
|
|
|
1694 #I FUCKED WITH THE MCC TABLE AND NEED TO FINISH IT
|
|
|
1695
|
|
|
1696 ThisKinBlanks<-rep(1,times=17)
|
|
|
1697 #indx <- sapply(breast, is.factor)
|
|
|
1698 #ThisKinTable[indx] <- lapply(ThisKinTable[indx], function(x) as.character(x))
|
|
|
1699 ThisKinTable$SetOfAAs<-as.character(ThisKinTable$SetOfAAs)
|
|
|
1700
|
|
|
1701 #ThisKinTest<-rbind.data.frame(ThisKinTable,ThisKinBlanks)
|
|
|
1702 ThisKinTable<-rbind.data.frame(ThisKinTable,ThisKinBlanks)
|
|
|
1703
|
|
|
1704 NegativeScores<-rep(NA,times=nrow(NegativeSubstrateList))
|
|
|
1705 NegativeWeirdScores<-rep(NA,times=nrow(NegativeSubstrateList))
|
|
|
1706 for (v in 1:nrow(NegativeSubstrateList)) {
|
|
|
1707 motif<-NegativeSubstrateList[v,2]
|
|
|
1708 motif<-unlist(strsplit(motif,""))
|
|
|
1709 #if (length(motif)<9){print(v)}}
|
|
|
1710 # motif[1] <- sapply(motif[1], function (x) aa_props[x])
|
|
|
1711 # motif[2] <- sapply(motif[2], function (x) aa_props[x])
|
|
|
1712 # motif[3] <- sapply(motif[3], function (x) aa_props[x])
|
|
|
1713 # motif[4] <- sapply(motif[4], function (x) aa_props[x])
|
|
|
1714 # motif[5] <- sapply(motif[5], function (x) aa_props[x])
|
|
|
1715 # motif[6] <- sapply(motif[6], function (x) aa_props[x])
|
|
|
1716 # motif[7] <- sapply(motif[7], function (x) aa_props[x])
|
|
|
1717 # motif[8] <- sapply(motif[8], function (x) aa_props[x])
|
|
|
1718 # motif[9] <- sapply(motif[9], function (x) aa_props[x])
|
|
|
1719 motif<- gsub(" ","O",motif)
|
|
|
1720 motif <- sapply(motif, function (x) aa_props[x])
|
|
|
1721 Scoringpeptide<-motif
|
|
|
1722 Scoringpeptide<-Scoringpeptide+1
|
|
|
1723 ThisKinTableScore<-as.numeric(ThisKinTable[Scoringpeptide[1],3])*ThisKinTable[as.numeric(Scoringpeptide[2]),4]*ThisKinTable[as.numeric(Scoringpeptide[3]),5]*
|
|
|
1724 ThisKinTable[as.numeric(Scoringpeptide[4]),6]*ThisKinTable[as.numeric(Scoringpeptide[5]),7]*ThisKinTable[as.numeric(Scoringpeptide[6]),8]*ThisKinTable[as.numeric(Scoringpeptide[7]),9]*
|
|
|
1725 #ThisKinTable[as.numeric(Scoringpeptide[8]),10]*
|
|
|
1726 ThisKinTable[as.numeric(Scoringpeptide[9]),11]*ThisKinTable[as.numeric(Scoringpeptide[10]),12]*ThisKinTable[as.numeric(Scoringpeptide[11]),13]*
|
|
|
1727 ThisKinTable[as.numeric(Scoringpeptide[12]),14]*ThisKinTable[as.numeric(Scoringpeptide[13]),15]*ThisKinTable[as.numeric(Scoringpeptide[14]),16]*ThisKinTable[as.numeric(Scoringpeptide[15]),17]
|
|
|
1728 NegativeScores[v]<-ThisKinTableScore
|
|
|
1729 ThisKinTableScore<-(ThisKinTableScore/(ThisKinTableScore+1/as.numeric(NormalizationScore[2])))
|
|
|
1730 NegativeWeirdScores[v]<-ThisKinTableScore*100
|
|
|
1731 }
|
|
|
1732
|
|
|
1733 negativesubstrates<-NegativeSubstrateList[,2]
|
|
|
1734 NegativeWithScores<-cbind(negativesubstrates,as.character(NegativeScores),as.character(NegativeWeirdScores))
|
|
|
1735
|
|
|
1736
|
|
|
1737 #NEED TO HAVE THE NEGATIVE SUBSTRATES BE OUTPUTTED
|
|
|
1738
|
|
|
1739 PositiveScores<-rep(NA,times=nrow(ImportedSubstrateList))
|
|
|
1740 PositiveWeirdScores<-rep(NA,times=nrow(ImportedSubstrateList))
|
|
|
1741
|
|
|
1742 for (v in 1:nrow(ImportedSubstrateList)) {
|
|
|
1743 motif<-ImportedSubstrateList[v,4:18]
|
|
|
1744 motif<-unlist(motif)
|
|
|
1745 motif<- gsub("^$","O",motif)
|
|
|
1746 motif <- sapply(motif, function (x) aa_props[x])
|
|
|
1747 Scoringpeptide<-motif
|
|
|
1748 Scoringpeptide<-Scoringpeptide+1
|
|
|
1749 ThisKinTableScore<-as.numeric(ThisKinTable[Scoringpeptide[1],3])*ThisKinTable[as.numeric(Scoringpeptide[2]),4]*ThisKinTable[as.numeric(Scoringpeptide[3]),5]*
|
|
|
1750 ThisKinTable[as.numeric(Scoringpeptide[4]),6]*ThisKinTable[as.numeric(Scoringpeptide[5]),7]*ThisKinTable[as.numeric(Scoringpeptide[6]),8]*ThisKinTable[as.numeric(Scoringpeptide[7]),9]*
|
|
|
1751 #ThisKinTable[as.numeric(Scoringpeptide[8]),10]*
|
|
|
1752 ThisKinTable[as.numeric(Scoringpeptide[9]),11]*ThisKinTable[as.numeric(Scoringpeptide[10]),12]*ThisKinTable[as.numeric(Scoringpeptide[11]),13]*
|
|
|
1753 ThisKinTable[as.numeric(Scoringpeptide[12]),14]*ThisKinTable[as.numeric(Scoringpeptide[13]),15]*ThisKinTable[as.numeric(Scoringpeptide[14]),16]*ThisKinTable[as.numeric(Scoringpeptide[15]),17]
|
|
|
1754
|
|
|
1755 PositiveScores[v]<-ThisKinTableScore
|
|
|
1756 ThisKinTableScore<-(ThisKinTableScore/(ThisKinTableScore+1/as.numeric(NormalizationScore[2])))
|
|
|
1757 PositiveWeirdScores[v]<-ThisKinTableScore*100
|
|
|
1758 }
|
|
|
1759
|
|
|
1760 positivesubstrates<-ImportedSubstrateList[,4:18]
|
|
|
1761 positivewithscores<-cbind.data.frame(positivesubstrates,PositiveScores,PositiveWeirdScores)
|
|
|
1762
|
|
|
1763
|
|
|
1764 #write down the transient transfection SOP and what we will be doing with them
|
|
|
1765 #write down the vector names I will be using
|
|
|
1766 #write down something about transforming bacteria and with what
|
|
|
1767
|
|
|
1768 #90% whatevernness
|
|
|
1769 # TPninetyone<-length(PositiveWeirdScores[PositiveWeirdScores>=0.91])
|
|
|
1770 # Senseninetyone<-TPninetyone/nrow(positivesubstrates)
|
|
|
1771 #
|
|
|
1772 # TNninetyone<-length(NegativeWeirdScores[NegativeWeirdScores<91])
|
|
|
1773 # Specninetyone<-TNninetyone/100
|
|
|
1774
|
|
|
1775 #create the MCC table
|
|
|
1776
|
|
|
1777 threshold<-c(1:100,(1:9)/10,(1:9)/100,0,-.1)
|
|
|
1778 threshold<-threshold[order(threshold,decreasing = TRUE)]
|
|
|
1779 threshold
|
|
|
1780
|
|
|
1781 Truepositives<-c(1:120)
|
|
|
1782 Falsenegatives<-c(1:120)
|
|
|
1783 Sensitivity<-c(1:120)
|
|
|
1784 TrueNegatives<-c(1:120)
|
|
|
1785 FalsePositives<-c(1:120)
|
|
|
1786 One_Minus_Specificity<-c(1:120)
|
|
|
1787 Accuracy<-c(1:120)
|
|
|
1788 MCC<-c(1:120)
|
|
|
1789 EER<-c(1:120)
|
|
|
1790 FalsePositiveRate<-c(1:120)
|
|
|
1791 Precision<-c(1:120)
|
|
|
1792 F_One_Half<-c(1:120)
|
|
|
1793 F_One<-c(1:120)
|
|
|
1794 F_Two<-c(1:120)
|
|
|
1795
|
|
|
1796 #MAKE DAMN SURE THAT THE ACCESSION NUMBERS FOLLOW THE MOTIFS
|
|
|
1797
|
|
|
1798 for (z in 1:120) {
|
|
|
1799 thres<-threshold[z]
|
|
|
1800 Truepositives[z]<-length(PositiveWeirdScores[PositiveWeirdScores>=(thres)])
|
|
|
1801 Falsenegatives[z]<-nrow(positivesubstrates)-Truepositives[z]
|
|
|
1802 Sensitivity[z]<-Truepositives[z]/(Falsenegatives[z]+Truepositives[z])
|
|
|
1803 TrueNegatives[z]<-length(NegativeWeirdScores[NegativeWeirdScores<(thres)])
|
|
|
1804 # at thresh 100 this should be 0, because it is total minus true negatives
|
|
|
1805 FalsePositives[z]<-nrow(NegativeSubstrateList)-TrueNegatives[z]
|
|
|
1806 One_Minus_Specificity[z]<-1-(TrueNegatives[z]/(FalsePositives[z]+TrueNegatives[z]))
|
|
|
1807 Accuracy[z]<-100*(Truepositives[z]+TrueNegatives[z])/(Falsenegatives[z]+FalsePositives[z]+TrueNegatives[z]+Truepositives[z])
|
|
|
1808 MCC[z]<-((Truepositives[z]*TrueNegatives[z])-(Falsenegatives[z]*FalsePositives[z]))/sqrt(round(round(Truepositives[z]+Falsenegatives[z])*round(TrueNegatives[z]+FalsePositives[z])*round(Truepositives[z]+FalsePositives[z])*round(TrueNegatives[z]+Falsenegatives[z])))
|
|
|
1809 EER[z]<-(FalsePositives[z]+Falsenegatives[z])/(Truepositives[z]+TrueNegatives[z]+FalsePositives[z]+Falsenegatives[z])
|
|
|
1810 Precision[z]<-Truepositives[z]/(Truepositives[z]+FalsePositives[z])
|
|
|
1811 F_One_Half[z]<-(1.5*Precision[z]*Sensitivity[z])/(.25*Precision[z]+Sensitivity[z])
|
|
|
1812 F_One<-(1*Precision[z]*Sensitivity[z])/(Precision[z]+Sensitivity[z])
|
|
|
1813 F_Two<-(5*Precision[z]*Sensitivity[z])/(4*Precision[z]+Sensitivity[z])
|
|
|
1814 FalsePositiveRate[z]<-FalsePositives[z]/(TrueNegatives[z]+FalsePositives[z])
|
|
|
1815 }
|
|
|
1816 Characterization<-cbind.data.frame(threshold,Truepositives,Falsenegatives,Sensitivity,TrueNegatives,FalsePositives,One_Minus_Specificity,MCC,EER,Precision,FalsePositiveRate,F_One_Half,F_One,F_Two)
|
|
|
1817
|
|
|
1818 positiveheader<-c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,"RPMS","PMS")
|
|
|
1819 positivewithscores<-rbind.data.frame(positiveheader,positivewithscores)
|
|
|
1820
|
|
|
1821 negativeheader<-c("Substrate","RPMS","PMS")
|
|
|
1822 colnames(NegativeWithScores)<-negativeheader
|
|
|
1823
|
|
|
1824 # write.xlsx(NegativeWithScores,file = FILENAME, sheetName = "Negative Sequences Scored",col.names = TRUE,row.names = FALSE,append = TRUE)
|
|
|
1825 # write.xlsx(Characterization,file = FILENAME,sheetName = "Characterization Table",col.names = TRUE,row.names = FALSE,append = TRUE)
|
|
|
1826 # write.xlsx(RanksPeptides,file = FILENAME,sheetName = "Ranked Generated Peptides",col.names = FALSE,row.names = FALSE,append = TRUE)
|
|
|
1827 # write.xlsx(positivewithscores,file = FILENAME, sheetName = "Positive Sequences Scored",col.names = FALSE,row.names = FALSE,append = TRUE)
|
|
|
1828 write.table(x=c("Characterzation Table"),file = FILENAME2, col.names = FALSE,row.names = FALSE, append = TRUE,sep = ",")
|
|
|
1829 header<-colnames(Characterization)
|
|
|
1830 Characterization<-rbind.data.frame(header,Characterization)
|
|
|
1831 write.table(Characterization,file = FILENAME2, col.names = FALSE,row.names = FALSE, append = TRUE,sep = ",")
|
|
|
1832
|
|
|
1833 # header<-colnames(RanksPeptides)
|
|
|
1834 # RanksPeptides<-rbind.data.frame(header,RanksPeptides)
|
|
|
1835 write.table(x="Off Target Kinase activity (your kinase of interest should have zeros here because it is ON-target)",file = FILENAME3,append = FALSE,row.names = FALSE,col.names = TRUE,sep = ",")
|
|
|
1836 write.table(RanksPeptides,file = FILENAME3,append = FALSE,row.names = FALSE,col.names = TRUE,sep = ",")
|
|
|
1837
|
|
|
1838
|
|
|
1839 PositivesWithScores<-as.data.frame(ImportedSubstrateList)
|
|
|
1840 PositiveOutput<-cbind(PositivesWithScores,PositiveWeirdScores)
|
|
|
1841 write.table(PositiveOutput, file = FILENAME4, sep = ",", na="",row.names=FALSE)
|
|
|
1842
|
|
|
1843 NegativeOutput<-as.data.frame(NegativeSubstrateList)
|
|
|
1844 NegativeOutput<-cbind(NegativeOutput,NegativeWeirdScores)
|
|
|
1845 write.table(NegativeOutput,file = FILENAME5,sep = ",",na="",row.names = FALSE) |
