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1 FirstSubstrateSet<- read.csv("input1.csv", stringsAsFactors=FALSE)
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2 Firstsubbackfreq<- read.csv("input2.csv", header=FALSE, stringsAsFactors=FALSE)
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3
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4 SecondSubstrateSet<- read.csv("input3.csv", stringsAsFactors=FALSE)
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5 Secondsubbackfreq<- read.csv("input4.csv", header=FALSE, stringsAsFactors=FALSE)
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6
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7 ThirdSubstrateSet<- read.csv("input5.csv", stringsAsFactors=FALSE)
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8 Thirdsubbackfreq<- read.csv("input6.csv", header=FALSE, stringsAsFactors=FALSE)
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9
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10
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11 args = commandArgs(trailingOnly=TRUE)
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12
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13 print(args[1])
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14 print(args[2])
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15 print(args[3])
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16
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17
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18 #ff you want ONLY FULL MOTIFS, put "YES" here, please use all caps
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19 FullMotifsOnly_questionmark<-args[1]
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20 #If you want ONLY TRUNCATED MOTIFS, put "YES" here, please use all caps
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21 TruncatedMotifsOnly_questionmark<-args[2]
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22 #if you want to find the overlap, put a "YES" here (all caps), if you want to find the non-overlap, put "NO" (all caps)
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23 Are_You_Looking_For_Commonality<-args[3]
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24
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25
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26 #then put the names of your output files here
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27 Shared_motifs_table<-"sharedmotifs.csv"
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28 Shared_subbackfreq_table<-"sharedSBF.csv"
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29
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30 # Shared_motifs_table<-"Shared motifs 7-27-17.csv"
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31 # Shared_subbackfreq_table<-"SubstrateBackgrounFrequency-for-shared-motifs 4 7-27-17.csv"
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32
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33 First_unshared_motifs_table<-"R1 substrates.csv"
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34 First_unshared_subbackfreq<-"R1 SBF.csv"
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35
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36 Second_unshared_motifs_table<-"R2 subs.csv"
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37 Second_unshared_subbackfreq<-"R2 SBf.csv"
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38
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39 Third_unshared_motifs_table<-"R3 subs.csv"
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40 Third_unshared_subbackfreq<-"R3 SBF.csv"
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41
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42 #final note, this code is going to be unworkable if you want to make a Venn diagram of more than 3 circles. I think I'll poke around
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43 #other languages to see if any of them can do it.
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44 ####################################################################################################################################
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45
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46
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47
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48
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49
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50 Firstx<-rep("x",times=nrow(FirstSubstrateSet))
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51 FirstST<-FirstSubstrateSet[,11]
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52 FirstxST<-cbind(Firstx,FirstST)
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53 FirstxST<-as.data.frame(FirstxST)
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54 FirstxST<-within(FirstxST, x <- paste(Firstx,FirstST,sep=""))
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55 FirstSubstrateSet[,11]<-FirstxST[,3]
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56
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57 Secondx<-rep("x",times=nrow(SecondSubstrateSet))
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58 SecondST<-SecondSubstrateSet[,11]
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59 SecondxST<-cbind(Secondx,SecondST)
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60 SecondxST<-as.data.frame(SecondxST)
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61 SecondxST<-within(SecondxST, x <- paste(Secondx,SecondST,sep=""))
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62 SecondSubstrateSet[,11]<-SecondxST[,3]
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63
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64 Thirdx<-rep("x",times=nrow(ThirdSubstrateSet))
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65 ThirdST<-ThirdSubstrateSet[,11]
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66 ThirdxST<-cbind(Thirdx,ThirdST)
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67 ThirdxST<-as.data.frame(ThirdxST)
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68 ThirdxST<-within(ThirdxST, x <- paste(Thirdx,ThirdST,sep=""))
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69 ThirdSubstrateSet[,11]<-ThirdxST[,3]
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70
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71
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72
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73
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74
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75
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76
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77
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78
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79
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80 ####################################################################################################################################
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81 ####################################################################################################################################
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82 # better version of this code written in C: what happens when two kinases share a motif, but they found that motif in two
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83 # separate proteins thus two separate accession numbers?
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84 # It should actually output the shared motif and BOTH accession numbers. Right now it does not, it only maps out the second
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85 # accession number. So that needs to be fixed BUT you need to keep the commonality between a motif and its accession number
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86 ####################################################################################################################################
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87 ####################################################################################################################################
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88 ####################################################################################################################################
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89 ####################################################################################################################################
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90
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91 #Create the motif sets, deciding wether or not you're looking for truncated or full here
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92 #full only
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93 if (Are_You_Looking_For_Commonality=="YES"){
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94 if (FullMotifsOnly_questionmark=="YES"){
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95 FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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96 FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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97 leftspaces<-c()
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98 rightspaces<-c()
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99 for (i in 1:nrow(FirstSubstrateSet)){
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100 FTLwtletters<-FirstSubstrateSet[i,4:18]
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101 FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
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102 FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
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103
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104
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105 YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
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106 YYYposition <- match(x = "x", table = YYYmotif)
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107 #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are
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108 #just 3 letters to the left of x
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109
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110 YYYLettersToTheLeft <- YYYposition - 1
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111 #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
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112 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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113 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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114 #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
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115 #variable the user puts in is
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116
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117 if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) {
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118 motif<-YYYmotif
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119 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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120 motif<-motif[!motif %in% "x"]
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121 motif<-paste(motif, sep="", collapse="")
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122 FTLwtletters<-motif
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123 FTLwtmotifs[i,1]<-FTLwtletters
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124 FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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125
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126 }
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127
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128 }
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129 # FTLwtmotifs <- FTLwtmotifs[!is.na(FTLwtmotifs)]
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130 # FTLwtmotifs<-matrix(FTLwtmotifs,ncol = 1)
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131 #
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132
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133 D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
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134 D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
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135
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136 for (i in 1:nrow(SecondSubstrateSet)){
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137 D835letters<-SecondSubstrateSet[i,4:18]
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138 D835letters<-D835letters[D835letters !="XXXXX"]
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139 D835letters<-paste(D835letters, sep="", collapse="")
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140
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141
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142 YYYmotif <- unlist(strsplit(D835letters, split = ""))
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143 YYYposition <- match(x = "x", table = YYYmotif)
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144 #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are
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145 #just 3 letters to the left of x
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146
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147 YYYLettersToTheLeft <- YYYposition - 1
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148 #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
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149 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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150 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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151 #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
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152 #variable the user puts in is
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153
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154 if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) {
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155 motif<-YYYmotif
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156 #add blank spaces if the motif has less than 4 letters to the left/right
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157 motif<-c(leftspaces,YYYmotif,rightspaces)
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158 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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159 motif<-motif[!motif %in% "x"]
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160 motif<-paste(motif, sep="", collapse="")
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161 D835letters<-motif
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162 D835Ymotifs[i,1]<-D835letters
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163 D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
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164
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165 }
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166 }
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167
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168 ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
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169 ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
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170
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171 for (i in 1:nrow(ThirdSubstrateSet)){
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172 ITDletters<-ThirdSubstrateSet[i,4:18]
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173 ITDletters<-ITDletters[ITDletters !="XXXXX"]
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174 ITDletters<-paste(ITDletters, sep="", collapse="")
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175 YYYmotif <- unlist(strsplit(ITDletters, split = ""))
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176 YYYposition <- match(x = "x", table = YYYmotif)
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177 #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are
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178 #just 3 letters to the left of x
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179
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180 YYYLettersToTheLeft <- YYYposition - 1
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181 #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
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182 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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183 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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184 #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
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185 #variable the user puts in is
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186
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187 if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) {
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188 motif<-YYYmotif
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189 #add blank spaces if the motif has less than 4 letters to the left/right
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190 motif<-c(leftspaces,YYYmotif,rightspaces)
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191 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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192 motif<-motif[!motif %in% "x"]
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193 motif<-paste(motif, sep="", collapse="")
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194 ITDletters<-motif
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195 ITDmotifs[i,1]<-ITDletters
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196 ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3]
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197
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198 }
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199 }
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200
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201 }
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202
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203 ##############################################3
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204 #Truncated only
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205 if (TruncatedMotifsOnly_questionmark=="YES"){
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206 FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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207 FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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208
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209 for (i in 1:nrow(FirstSubstrateSet)){
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210 FTLwtletters<-FirstSubstrateSet[i,4:18]
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211 FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
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212 FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
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213
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214
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215 YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
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216 YYYposition <- match(x = "x", table = YYYmotif)
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217 #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are
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218 #just 3 letters to the left of x
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219
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220 YYYLettersToTheLeft <- YYYposition - 1
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221 #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
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222 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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223 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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224 #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
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225 #variable the user puts in is
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226
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227 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
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228 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
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229 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
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230 #add blank spaces if the motif has less than 4 letters to the left/right
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231 motif<-c(leftspaces,YYYmotif,rightspaces)
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232 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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233 motif<-motif[!motif %in% "x"]
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234 motif<-paste(motif, sep="", collapse="")
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235 FTLwtletters<-motif
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236 FTLwtmotifs[i,1]<-FTLwtletters
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237 FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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238 }
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239
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240 }
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241
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242 D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
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243 D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
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244
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245 for (i in 1:nrow(SecondSubstrateSet)){
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246 D835letters<-SecondSubstrateSet[i,4:18]
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247 D835letters<-D835letters[D835letters !="XXXXX"]
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248 D835letters<-paste(D835letters, sep="", collapse="")
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249
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250
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251 YYYmotif <- unlist(strsplit(D835letters, split = ""))
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252 YYYposition <- match(x = "x", table = YYYmotif)
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253 #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are
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254 #just 3 letters to the left of x
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255
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256 YYYLettersToTheLeft <- YYYposition - 1
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257 #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
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258 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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259 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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260 #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
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261 #variable the user puts in is
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262
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263 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
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264 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
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265 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
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266 #add blank spaces if the motif has less than 4 letters to the left/right
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267 motif<-c(leftspaces,YYYmotif,rightspaces)
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268 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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269 motif<-motif[!motif %in% "x"]
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270 motif<-paste(motif, sep="", collapse="")
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271 D835letters<-motif
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272 D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
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273 D835Ymotifs[i,1]<-D835letters
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274 }
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275 }
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276
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277 ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
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278 ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
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279
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280 for (i in 1:nrow(ThirdSubstrateSet)){
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281 ITDletters<-ThirdSubstrateSet[i,4:18]
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282 ITDletters<-ITDletters[ITDletters !="XXXXX"]
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283 ITDletters<-paste(ITDletters, sep="", collapse="")
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284 YYYmotif <- unlist(strsplit(ITDletters, split = ""))
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285 YYYposition <- match(x = "x", table = YYYmotif)
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286 #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are
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287 #just 3 letters to the left of x
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288
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289 YYYLettersToTheLeft <- YYYposition - 1
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290 #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
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291 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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292 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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293 #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
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294 #variable the user puts in is
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295
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296 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
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297 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
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298 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
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299 #add blank spaces if the motif has less than 4 letters to the left/right
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300 motif<-c(leftspaces,YYYmotif,rightspaces)
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301 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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302 motif<-motif[!motif %in% "x"]
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303 motif<-paste(motif, sep="", collapse="")
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304 ITDletters<-motif
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305 ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3]
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306 ITDmotifs[i,1]<-ITDletters
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307 }
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308 }
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309
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310 }
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311
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312 ###############################################
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313 #ALL motifs, full and truncated
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314
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315 if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){
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316 FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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317 FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
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318
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319 for (i in 1:nrow(FirstSubstrateSet)){
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320 FTLwtletters<-FirstSubstrateSet[i,4:18]
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321 FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
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322 FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
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323 leftspaces<-c()
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324 rightspaces<-c()
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325
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326 YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
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327 YYYposition <- match(x = "x", table = YYYmotif)
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328 #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are
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329 #just 3 letters to the left of x
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330
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331 YYYLettersToTheLeft <- YYYposition - 1
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332 #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
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333 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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334 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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335 #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
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336 #variable the user puts in is
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337
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338
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339 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
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340 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
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341 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
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342 #add blank spaces if the motif has less than 4 letters to the left/right
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343 motif<-c(leftspaces,YYYmotif,rightspaces)
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344 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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345 motif<-motif[!motif %in% "x"]
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346 motif<-paste(motif, sep="", collapse="")
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347 FTLwtletters<-motif
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348 FTLwtmotifs[i,1]<-FTLwtletters
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349 FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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350 }
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351
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352 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
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353 motif<-YYYmotif
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354 #add blank spaces if the motif has less than 4 letters to the left/right
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355 motif<-c(leftspaces,YYYmotif,rightspaces)
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356 #save that motif, which is the Y and +/- 4 amino acids, including truncation
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357 motif<-motif[!motif %in% "x"]
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358 motif<-paste(motif, sep="", collapse="")
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359 FTLwtletters<-motif
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360 FTLwtmotifs[i,1]<-FTLwtletters
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361 FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
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362
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363
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364 }
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365
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366 }
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367
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368 D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
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369 D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
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370
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371 for (i in 1:nrow(SecondSubstrateSet)){
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372 D835letters<-SecondSubstrateSet[i,4:18]
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373 D835letters<-D835letters[D835letters !="XXXXX"]
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374 D835letters<-paste(D835letters, sep="", collapse="")
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375 leftspaces<-c()
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376 rightspaces<-c()
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377
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378 YYYmotif <- unlist(strsplit(D835letters, split = ""))
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379 YYYposition <- match(x = "x", table = YYYmotif)
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380 #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are
|
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381 #just 3 letters to the left of x
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382
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383 YYYLettersToTheLeft <- YYYposition - 1
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|
|
384 #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
|
|
|
385 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
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386 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
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387 #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
|
|
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388 #variable the user puts in is
|
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389 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
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390 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
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|
391 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
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|
392 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
393 motif<-c(leftspaces,YYYmotif,rightspaces)
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|
394 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
395 motif<-motif[!motif %in% "x"]
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|
|
396 motif<-paste(motif, sep="", collapse="")
|
|
|
397 D835letters<-motif
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|
|
398 D835Ymotifs[i,1]<-D835letters
|
|
|
399 D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
|
|
|
400 }
|
|
|
401
|
|
|
402 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
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|
|
403 motif<-YYYmotif
|
|
|
404 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
405 motif<-c(leftspaces,YYYmotif,rightspaces)
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|
|
406 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
407 motif<-motif[!motif %in% "x"]
|
|
|
408 motif<-paste(motif, sep="", collapse="")
|
|
|
409 D835letters<-motif
|
|
|
410 D835Ymotifs[i,1]<-D835letters
|
|
|
411 D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
|
|
|
412 }
|
|
|
413 }
|
|
|
414
|
|
|
415
|
|
|
416 ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
|
|
|
417 ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
|
|
|
418
|
|
|
419 for (i in 1:nrow(ThirdSubstrateSet)){
|
|
|
420 ITDletters<-ThirdSubstrateSet[i,4:18]
|
|
|
421 ITDletters<-ITDletters[ITDletters !="XXXXX"]
|
|
|
422 ITDletters<-paste(ITDletters, sep="", collapse="")
|
|
|
423 YYYmotif <- unlist(strsplit(ITDletters, split = ""))
|
|
|
424 leftspaces<-c()
|
|
|
425 rightspaces<-c()
|
|
|
426 YYYposition <- match(x = "x", table = YYYmotif)
|
|
|
427 #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are
|
|
|
428 #just 3 letters to the left of x
|
|
|
429
|
|
|
430 YYYLettersToTheLeft <- YYYposition - 1
|
|
|
431 #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
|
|
|
432 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
|
|
|
433 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
|
|
|
434 #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
|
|
|
435 #variable the user puts in is
|
|
|
436 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
|
|
|
437 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
|
|
|
438 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
|
|
|
439 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
440 motif<-c(leftspaces,YYYmotif,rightspaces)
|
|
|
441 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
442 motif<-motif[!motif %in% "x"]
|
|
|
443 motif<-paste(motif, sep="", collapse="")
|
|
|
444 ITDletters<-motif
|
|
|
445 ITDmotifs[i,1]<-ITDletters
|
|
|
446 ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
|
|
|
447 }
|
|
|
448
|
|
|
449 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
|
|
|
450 motif<-YYYmotif
|
|
|
451 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
452 motif<-c(leftspaces,YYYmotif,rightspaces)
|
|
|
453 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
454 motif<-motif[!motif %in% "x"]
|
|
|
455 motif<-paste(motif, sep="", collapse="")
|
|
|
456 ITDletters<-motif
|
|
|
457 ITDmotifs[i,1]<-ITDletters
|
|
|
458 ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
|
|
|
459 }
|
|
|
460 }
|
|
|
461
|
|
|
462 }
|
|
|
463 #############################################################################################################################
|
|
|
464 #############################################################################################################################
|
|
|
465 #############################################################################################################################
|
|
|
466 #############################################################################################################################
|
|
|
467 #############################################################################################################################
|
|
|
468
|
|
|
469 #now look for either commonality or difference. Actually could you look for both...
|
|
|
470
|
|
|
471 if (Are_You_Looking_For_Commonality=="YES"){
|
|
|
472
|
|
|
473 columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1]))
|
|
|
474 columnalheader<-matrix(columnalheader,nrow = 1)
|
|
|
475 # write.table(x=columnalheader,
|
|
|
476 # file=Shared_subbackfreq_table,
|
|
|
477 # quote=FALSE, sep=",",
|
|
|
478 # row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
479
|
|
|
480 FirstOverlapmotifs<-c()
|
|
|
481 for (i in 1:nrow(ITDmotifs)){
|
|
|
482 for (j in 1:nrow(D835Ymotifs)){
|
|
|
483 if (is.na(ITDmotifs[i,1])!=TRUE&&is.na(D835Ymotifs[j,1])!=TRUE){
|
|
|
484 if (ITDmotifs[i,1]==D835Ymotifs[j,1]){
|
|
|
485 FirstOverlapmotifs<-c(FirstOverlapmotifs,D835Ymotifs[j,1])
|
|
|
486 }
|
|
|
487 }
|
|
|
488 }
|
|
|
489 }
|
|
|
490
|
|
|
491 AllAccessionNumbers<-c()
|
|
|
492 columnalheader<-c(rep(NA,36))
|
|
|
493 FinalMatrix<-matrix(data =columnalheader,nrow = 1)
|
|
|
494
|
|
|
495 FinalMotifs<-c(rep(NA,20))
|
|
|
496 FinalMotifsMatrix<-matrix(data = FinalMotifs,nrow = 1)
|
|
|
497
|
|
|
498
|
|
|
499 for (l in 1:length(FirstOverlapmotifs)) {
|
|
|
500 AccessionNumber<-00000000000
|
|
|
501 for (k in 1:nrow(FTLwtmotifs)) {
|
|
|
502 AccessionNumber<-0000000000000
|
|
|
503 if(is.na(FTLwtmotifs[k])!=TRUE){
|
|
|
504 #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
|
|
|
505 #destroyed immediately after use
|
|
|
506 if (FirstOverlapmotifs[l] == FTLwtmotifs[k]) {
|
|
|
507 substratematrix<-FirstSubstrateSet[k,1:20]
|
|
|
508 substratematrix<-as.matrix(substratematrix,nrow=1)
|
|
|
509 FinalMotifsMatrix<-rbind(FinalMotifsMatrix,substratematrix)
|
|
|
510 #when you find a match between the venn diagrams, save the substrate info you get into a matrix
|
|
|
511
|
|
|
512 AccessionNumber <- as.character(FirstSubstrateSet[k, 3])
|
|
|
513 #then take the accession number
|
|
|
514
|
|
|
515 for (m in 1:ncol(Firstsubbackfreq)) {
|
|
|
516 AN <- as.character(Firstsubbackfreq[1, m])
|
|
|
517 if (grepl(pattern = AN,
|
|
|
518 x = AccessionNumber,
|
|
|
519 fixed = TRUE) == TRUE) {
|
|
|
520 outputmatrix <- as.character(Firstsubbackfreq[, m])
|
|
|
521 outputmatrix <- matrix(outputmatrix, nrow = 1)
|
|
|
522 #with that accession number, find a match in the subbackfreq file and save it here
|
|
|
523 FinalMatrix<-rbind(FinalMatrix,outputmatrix)
|
|
|
524 }
|
|
|
525 }
|
|
|
526 }
|
|
|
527 }
|
|
|
528 }
|
|
|
529 }
|
|
|
530
|
|
|
531
|
|
|
532 TrueMatrix<-FinalMatrix[!duplicated(FinalMatrix),]
|
|
|
533 TrueFinalMotifsMatrix<-FinalMotifsMatrix[!duplicated(FinalMotifsMatrix),]
|
|
|
534
|
|
|
535 TrueFinalMotifsMatrix<-TrueFinalMotifsMatrix[2:nrow(TrueFinalMotifsMatrix),]
|
|
|
536 TrueMatrix<-TrueMatrix[2:nrow(TrueMatrix),]
|
|
|
537
|
|
|
538 write.table(
|
|
|
539 x = TrueFinalMotifsMatrix,
|
|
|
540 file = Shared_motifs_table,
|
|
|
541 quote = FALSE,
|
|
|
542 sep = ",",
|
|
|
543 row.names = FALSE,
|
|
|
544 col.names = TRUE,
|
|
|
545 na = "",
|
|
|
546 append = FALSE
|
|
|
547 )
|
|
|
548
|
|
|
549 #TrueMatrix<-t(TrueMatrix)
|
|
|
550 columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1]))
|
|
|
551 columnalheader<-matrix(columnalheader,nrow = 1)
|
|
|
552
|
|
|
553 TrueMatrix<-rbind(columnalheader,TrueMatrix)
|
|
|
554 TrueMatrix<-t(TrueMatrix)
|
|
|
555
|
|
|
556 write.table(
|
|
|
557 x = TrueMatrix,
|
|
|
558 file = Shared_subbackfreq_table,
|
|
|
559 quote = FALSE,
|
|
|
560 sep = ",",
|
|
|
561 row.names = FALSE,
|
|
|
562 col.names = FALSE,
|
|
|
563 na = "",
|
|
|
564 append = TRUE
|
|
|
565 )
|
|
|
566 }
|
|
|
567 }
|
|
|
568
|
|
|
569 if (Are_You_Looking_For_Commonality=="NO"){
|
|
|
570 if (FullMotifsOnly_questionmark=="YES"){
|
|
|
571 FTLwtmotifs=rep(NA,times=nrow(FirstSubstrateSet))
|
|
|
572 FTLwtAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet))
|
|
|
573 leftspaces<-c()
|
|
|
574 rightspaces<-c()
|
|
|
575 for (i in 1:nrow(FirstSubstrateSet)){
|
|
|
576 FTLwtletters<-FirstSubstrateSet[i,4:18]
|
|
|
577 FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
|
|
|
578 FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
|
|
|
579
|
|
|
580
|
|
|
581 YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
|
|
|
582 YYYposition <- match(x = "x", table = YYYmotif)
|
|
|
583 #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are
|
|
|
584 #just 3 letters to the left of x
|
|
|
585
|
|
|
586 YYYLettersToTheLeft <- YYYposition - 1
|
|
|
587 #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
|
|
|
588 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
|
|
|
589 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
|
|
|
590 #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
|
|
|
591 #variable the user puts in is
|
|
|
592
|
|
|
593 if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) {
|
|
|
594 motif<-YYYmotif
|
|
|
595 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
596 motif<-motif[!motif %in% "x"]
|
|
|
597 motif<-paste(motif, sep="", collapse="")
|
|
|
598 FTLwtletters<-motif
|
|
|
599 FTLwtmotifs[i]<-FTLwtletters
|
|
|
600 FTLwtAccessionNumbers[i]<-FirstSubstrateSet[i,3]
|
|
|
601 }
|
|
|
602
|
|
|
603 }
|
|
|
604 # FTLwtmotifs <- FTLwtmotifs[!is.na(FTLwtmotifs)]
|
|
|
605 # FTLwtmotifs<-matrix(FTLwtmotifs,ncol = 1)
|
|
|
606 #
|
|
|
607
|
|
|
608 D835Ymotifs=rep(NA,times=nrow(FirstSubstrateSet))
|
|
|
609 D835YAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet))
|
|
|
610
|
|
|
611 for (i in 1:nrow(SecondSubstrateSet)){
|
|
|
612 D835letters<-SecondSubstrateSet[i,4:18]
|
|
|
613 D835letters<-D835letters[D835letters !="XXXXX"]
|
|
|
614 D835letters<-paste(D835letters, sep="", collapse="")
|
|
|
615
|
|
|
616
|
|
|
617 YYYmotif <- unlist(strsplit(D835letters, split = ""))
|
|
|
618 YYYposition <- match(x = "x", table = YYYmotif)
|
|
|
619 #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are
|
|
|
620 #just 3 letters to the left of x
|
|
|
621
|
|
|
622 YYYLettersToTheLeft <- YYYposition - 1
|
|
|
623 #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
|
|
|
624 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
|
|
|
625 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
|
|
|
626 #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
|
|
|
627 #variable the user puts in is
|
|
|
628
|
|
|
629 if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) {
|
|
|
630 motif<-YYYmotif
|
|
|
631 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
632 motif<-c(leftspaces,YYYmotif,rightspaces)
|
|
|
633 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
634 motif<-motif[!motif %in% "x"]
|
|
|
635 motif<-paste(motif, sep="", collapse="")
|
|
|
636 D835letters<-motif
|
|
|
637 D835Ymotifs[i]<-D835letters
|
|
|
638 D835YAccessionNumbers[i]<-SecondSubstrateSet[i,3]
|
|
|
639 }
|
|
|
640 }
|
|
|
641
|
|
|
642 ITDmotifs=rep(NA,times=nrow(FirstSubstrateSet))
|
|
|
643 ITDAccessionNumbers=rep(NA,times=nrow(FirstSubstrateSet))
|
|
|
644
|
|
|
645 for (i in 1:nrow(ThirdSubstrateSet)){
|
|
|
646 ITDletters<-ThirdSubstrateSet[i,4:18]
|
|
|
647 ITDletters<-ITDletters[ITDletters !="XXXXX"]
|
|
|
648 ITDletters<-paste(ITDletters, sep="", collapse="")
|
|
|
649 YYYmotif <- unlist(strsplit(ITDletters, split = ""))
|
|
|
650 YYYposition <- match(x = "x", table = YYYmotif)
|
|
|
651 #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are
|
|
|
652 #just 3 letters to the left of x
|
|
|
653
|
|
|
654 YYYLettersToTheLeft <- YYYposition - 1
|
|
|
655 #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
|
|
|
656 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
|
|
|
657 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
|
|
|
658 #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
|
|
|
659 #variable the user puts in is
|
|
|
660
|
|
|
661 if (YYYLettersToTheLeft > 6 && YYYLettersToTheRight > 6) {
|
|
|
662 motif<-YYYmotif
|
|
|
663 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
664 motif<-c(leftspaces,YYYmotif,rightspaces)
|
|
|
665 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
666 motif<-motif[!motif %in% "x"]
|
|
|
667 motif<-paste(motif, sep="", collapse="")
|
|
|
668 ITDletters<-motif
|
|
|
669 ITDmotifs[i]<-ITDletters
|
|
|
670 ITDAccessionNumbers[i]<-ThirdSubstrateSet[i,3]
|
|
|
671
|
|
|
672 }
|
|
|
673 }
|
|
|
674 names(ITDmotifs)<-ITDAccessionNumbers
|
|
|
675 names(D835Ymotifs)<-D835YAccessionNumbers
|
|
|
676 names(FTLwtmotifs)<-FTLwtAccessionNumbers
|
|
|
677 }
|
|
|
678
|
|
|
679
|
|
|
680 ##############################################3
|
|
|
681 #Truncated only
|
|
|
682 if (TruncatedMotifsOnly_questionmark=="YES"){
|
|
|
683 FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
|
|
|
684 FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
|
|
|
685
|
|
|
686 for (i in 1:nrow(FirstSubstrateSet)){
|
|
|
687 FTLwtletters<-FirstSubstrateSet[i,4:18]
|
|
|
688 FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
|
|
|
689 FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
|
|
|
690
|
|
|
691
|
|
|
692 YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
|
|
|
693 YYYposition <- match(x = "x", table = YYYmotif)
|
|
|
694 #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are
|
|
|
695 #just 3 letters to the left of x
|
|
|
696
|
|
|
697 YYYLettersToTheLeft <- YYYposition - 1
|
|
|
698 #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
|
|
|
699 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
|
|
|
700 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
|
|
|
701 #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
|
|
|
702 #variable the user puts in is
|
|
|
703
|
|
|
704 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
|
|
|
705 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
|
|
|
706 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
|
|
|
707 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
708 motif<-c(leftspaces,YYYmotif,rightspaces)
|
|
|
709 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
710 motif<-motif[!motif %in% "x"]
|
|
|
711 motif<-paste(motif, sep="", collapse="")
|
|
|
712 FTLwtletters<-motif
|
|
|
713 FTLwtmotifs[i,1]<-FTLwtletters
|
|
|
714 FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
|
|
|
715 }
|
|
|
716
|
|
|
717 }
|
|
|
718
|
|
|
719 D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
|
|
|
720 D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
|
|
|
721 i=2
|
|
|
722 for (i in 1:nrow(SecondSubstrateSet)){
|
|
|
723 D835letters<-SecondSubstrateSet[i,4:18]
|
|
|
724 D835letters<-D835letters[D835letters !="XXXXX"]
|
|
|
725 D835letters<-paste(D835letters, sep="", collapse="")
|
|
|
726
|
|
|
727
|
|
|
728 YYYmotif <- unlist(strsplit(D835letters, split = ""))
|
|
|
729 YYYposition <- match(x = "x", table = YYYmotif)
|
|
|
730 #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are
|
|
|
731 #just 3 letters to the left of x
|
|
|
732
|
|
|
733 YYYLettersToTheLeft <- YYYposition - 1
|
|
|
734 #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
|
|
|
735 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
|
|
|
736 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
|
|
|
737 #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
|
|
|
738 #variable the user puts in is
|
|
|
739
|
|
|
740 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
|
|
|
741 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
|
|
|
742 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
|
|
|
743 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
744 motif<-c(leftspaces,YYYmotif,rightspaces)
|
|
|
745 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
746 motif<-motif[!motif %in% "x"]
|
|
|
747 motif<-paste(motif, sep="", collapse="")
|
|
|
748 D835letters<-motif
|
|
|
749 D835YAccessionNumbers[i,1]<-SecondSubstrateSet[i,3]
|
|
|
750 D835Ymotifs[i,1]<-D835letters
|
|
|
751 }
|
|
|
752 }
|
|
|
753
|
|
|
754 ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
|
|
|
755 ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
|
|
|
756
|
|
|
757 for (i in 1:nrow(ThirdSubstrateSet)){
|
|
|
758 ITDletters<-ThirdSubstrateSet[i,4:18]
|
|
|
759 ITDletters<-ITDletters[ITDletters !="XXXXX"]
|
|
|
760 ITDletters<-paste(ITDletters, sep="", collapse="")
|
|
|
761 YYYmotif <- unlist(strsplit(ITDletters, split = ""))
|
|
|
762 YYYposition <- match(x = "x", table = YYYmotif)
|
|
|
763 #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are
|
|
|
764 #just 3 letters to the left of x
|
|
|
765
|
|
|
766 YYYLettersToTheLeft <- YYYposition - 1
|
|
|
767 #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
|
|
|
768 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
|
|
|
769 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
|
|
|
770 #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
|
|
|
771 #variable the user puts in is
|
|
|
772
|
|
|
773 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
|
|
|
774 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
|
|
|
775 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
|
|
|
776 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
777 motif<-c(leftspaces,YYYmotif,rightspaces)
|
|
|
778 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
779 motif<-motif[!motif %in% "x"]
|
|
|
780 motif<-paste(motif, sep="", collapse="")
|
|
|
781 ITDletters<-motif
|
|
|
782 ITDAccessionNumbers[i,1]<-ThirdSubstrateSet[i,3]
|
|
|
783 ITDmotifs[i,1]<-ITDletters
|
|
|
784 }
|
|
|
785 }
|
|
|
786 names(FTLwtmotifs)<-FTLwtAccessionNumbers
|
|
|
787 names(D835Ymotifs)<-D835YAccessionNumbers
|
|
|
788 names(ITDmotifs)<-ITDAccessionNumbers
|
|
|
789 }
|
|
|
790
|
|
|
791 ###############################################
|
|
|
792 #ALL motifs, full and truncated
|
|
|
793
|
|
|
794 if (FullMotifsOnly_questionmark!="YES"&&TruncatedMotifsOnly_questionmark!="YES"){
|
|
|
795 FTLwtmotifs=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
|
|
|
796 FTLwtAccessionNumbers=matrix(,nrow = nrow(FirstSubstrateSet),ncol=1)
|
|
|
797
|
|
|
798 for (i in 1:nrow(FirstSubstrateSet)){
|
|
|
799 FTLwtletters<-FirstSubstrateSet[i,4:18]
|
|
|
800 FTLwtletters<-FTLwtletters[FTLwtletters !="XXXXX"]
|
|
|
801 FTLwtletters<-paste(FTLwtletters, sep="", collapse="")
|
|
|
802 leftspaces<-c()
|
|
|
803 rightspaces<-c()
|
|
|
804
|
|
|
805 YYYmotif <- unlist(strsplit(FTLwtletters, split = ""))
|
|
|
806 YYYposition <- match(x = "x", table = YYYmotif)
|
|
|
807 #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are
|
|
|
808 #just 3 letters to the left of x
|
|
|
809
|
|
|
810 YYYLettersToTheLeft <- YYYposition - 1
|
|
|
811 #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
|
|
|
812 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
|
|
|
813 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
|
|
|
814 #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
|
|
|
815 #variable the user puts in is
|
|
|
816
|
|
|
817
|
|
|
818 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
|
|
|
819 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
|
|
|
820 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
|
|
|
821 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
822 motif<-c(leftspaces,YYYmotif,rightspaces)
|
|
|
823 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
824 motif<-motif[!motif %in% "x"]
|
|
|
825 motif<-paste(motif, sep="", collapse="")
|
|
|
826 FTLwtletters<-motif
|
|
|
827 FTLwtmotifs[i,1]<-FTLwtletters
|
|
|
828 FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
|
|
|
829 }
|
|
|
830
|
|
|
831 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
|
|
|
832 motif<-YYYmotif
|
|
|
833 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
834 motif<-c(leftspaces,YYYmotif,rightspaces)
|
|
|
835 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
836 motif<-motif[!motif %in% "x"]
|
|
|
837 motif<-paste(motif, sep="", collapse="")
|
|
|
838 FTLwtletters<-motif
|
|
|
839 FTLwtmotifs[i,1]<-FTLwtletters
|
|
|
840 FTLwtAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
|
|
|
841
|
|
|
842
|
|
|
843 }
|
|
|
844
|
|
|
845 }
|
|
|
846
|
|
|
847 D835Ymotifs=matrix(,nrow = nrow(SecondSubstrateSet),ncol=1)
|
|
|
848 D835YAccessionNumbers<-matrix(,nrow = nrow(SecondSubstrateSet),ncol = 1)
|
|
|
849
|
|
|
850 for (i in 1:nrow(SecondSubstrateSet)){
|
|
|
851 D835letters<-SecondSubstrateSet[i,4:18]
|
|
|
852 D835letters<-D835letters[D835letters !="XXXXX"]
|
|
|
853 D835letters<-paste(D835letters, sep="", collapse="")
|
|
|
854 leftspaces<-c()
|
|
|
855 rightspaces<-c()
|
|
|
856
|
|
|
857 YYYmotif <- unlist(strsplit(D835letters, split = ""))
|
|
|
858 YYYposition <- match(x = "x", table = YYYmotif)
|
|
|
859 #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are
|
|
|
860 #just 3 letters to the left of x
|
|
|
861
|
|
|
862 YYYLettersToTheLeft <- YYYposition - 1
|
|
|
863 #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
|
|
|
864 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
|
|
|
865 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
|
|
|
866 #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
|
|
|
867 #variable the user puts in is
|
|
|
868 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
|
|
|
869 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
|
|
|
870 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
|
|
|
871 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
872 motif<-c(leftspaces,YYYmotif,rightspaces)
|
|
|
873 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
874 motif<-motif[!motif %in% "x"]
|
|
|
875 motif<-paste(motif, sep="", collapse="")
|
|
|
876 D835letters<-motif
|
|
|
877 D835Ymotifs[i,1]<-D835letters
|
|
|
878 D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
|
|
|
879 }
|
|
|
880
|
|
|
881 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
|
|
|
882 motif<-YYYmotif
|
|
|
883 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
884 motif<-c(leftspaces,YYYmotif,rightspaces)
|
|
|
885 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
886 motif<-motif[!motif %in% "x"]
|
|
|
887 motif<-paste(motif, sep="", collapse="")
|
|
|
888 D835letters<-motif
|
|
|
889 D835Ymotifs[i,1]<-D835letters
|
|
|
890 D835YAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
|
|
|
891 }
|
|
|
892 }
|
|
|
893
|
|
|
894
|
|
|
895 ITDmotifs=matrix(,nrow = nrow(ThirdSubstrateSet),ncol=1)
|
|
|
896 ITDAccessionNumbers<-matrix(,nrow = nrow(ThirdSubstrateSet))
|
|
|
897
|
|
|
898 for (i in 1:nrow(ThirdSubstrateSet)){
|
|
|
899 ITDletters<-ThirdSubstrateSet[i,4:18]
|
|
|
900 ITDletters<-ITDletters[ITDletters !="XXXXX"]
|
|
|
901 ITDletters<-paste(ITDletters, sep="", collapse="")
|
|
|
902 YYYmotif <- unlist(strsplit(ITDletters, split = ""))
|
|
|
903 leftspaces<-c()
|
|
|
904 rightspaces<-c()
|
|
|
905 YYYposition <- match(x = "x", table = YYYmotif)
|
|
|
906 #position itself tells me how much is to the left of that X by what it's number is. x at position 4 tells me that there are
|
|
|
907 #just 3 letters to the left of x
|
|
|
908
|
|
|
909 YYYLettersToTheLeft <- YYYposition - 1
|
|
|
910 #how many letters to the right SHOULD just be length(motif)-position-1 if it's 5 long and x is at 3 then Y is at 4 and there is
|
|
|
911 #just 1 spot to the right of Y so LettersToTheRight<-1 because 5-3-1=1
|
|
|
912 YYYLettersToTheRight <- length(YYYmotif) - YYYposition - 1
|
|
|
913 #then sanity check, we're currently looking only at +/-4, but this spot allows for up to +/- 7 as well, just depends on what the
|
|
|
914 #variable the user puts in is
|
|
|
915 if (YYYLettersToTheLeft < 7 | YYYLettersToTheRight < 7) {
|
|
|
916 leftspaces<-rep(" ",times=(7-YYYLettersToTheLeft))
|
|
|
917 rightspaces<-rep(" ",times=7-(YYYLettersToTheRight))
|
|
|
918 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
919 motif<-c(leftspaces,YYYmotif,rightspaces)
|
|
|
920 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
921 motif<-motif[!motif %in% "x"]
|
|
|
922 motif<-paste(motif, sep="", collapse="")
|
|
|
923 ITDletters<-motif
|
|
|
924 ITDmotifs[i,1]<-ITDletters
|
|
|
925 ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
|
|
|
926 }
|
|
|
927
|
|
|
928 if(YYYLettersToTheLeft>6 && YYYLettersToTheRight>6){
|
|
|
929 motif<-YYYmotif
|
|
|
930 #add blank spaces if the motif has less than 4 letters to the left/right
|
|
|
931 motif<-c(leftspaces,YYYmotif,rightspaces)
|
|
|
932 #save that motif, which is the Y and +/- 4 amino acids, including truncation
|
|
|
933 motif<-motif[!motif %in% "x"]
|
|
|
934 motif<-paste(motif, sep="", collapse="")
|
|
|
935 ITDletters<-motif
|
|
|
936 ITDmotifs[i,1]<-ITDletters
|
|
|
937 ITDAccessionNumbers[i,1]<-FirstSubstrateSet[i,3]
|
|
|
938 }
|
|
|
939 }
|
|
|
940 names(FTLwtmotifs)<-FTLwtAccessionNumbers
|
|
|
941 names(D835Ymotifs)<-D835YAccessionNumbers
|
|
|
942 names(ITDmotifs)<-ITDAccessionNumbers
|
|
|
943 }
|
|
|
944
|
|
|
945
|
|
|
946 FTLwtmotifsFINAL<-FTLwtmotifs[!FTLwtmotifs %in% D835Ymotifs]
|
|
|
947 FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!FTLwtmotifsFINAL %in% ITDmotifs]
|
|
|
948 FTLwtmotifsFINAL<-FTLwtmotifsFINAL[!duplicated(FTLwtmotifsFINAL)]
|
|
|
949
|
|
|
950
|
|
|
951 ITDmotifsFINAL<-ITDmotifs[!ITDmotifs %in% D835Ymotifs]
|
|
|
952 ITDmotifsFINAL<-ITDmotifsFINAL[!ITDmotifsFINAL %in% FTLwtmotifs]
|
|
|
953 ITDmotifsFINAL<-ITDmotifsFINAL[!duplicated(ITDmotifsFINAL)]
|
|
|
954
|
|
|
955
|
|
|
956 D835YmotifsFINAL<-D835Ymotifs[!D835Ymotifs %in% FTLwtmotifs]
|
|
|
957 D835YmotifsFINAL<-D835YmotifsFINAL[!D835YmotifsFINAL %in% ITDmotifs]
|
|
|
958 D835YmotifsFINAL<-D835YmotifsFINAL[!duplicated(D835YmotifsFINAL)]
|
|
|
959
|
|
|
960
|
|
|
961 columnalheader<-c(rep(NA,36))
|
|
|
962 FTLFinalMatrix<-matrix(data =columnalheader,nrow = 1)
|
|
|
963
|
|
|
964 for (k in 1:length(FTLwtmotifsFINAL)) {
|
|
|
965 AN<-00000
|
|
|
966 #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
|
|
|
967 #destroyed immediately after use
|
|
|
968 for (m in 1:ncol(Firstsubbackfreq)) {
|
|
|
969 AN <- as.character(Firstsubbackfreq[1, m])
|
|
|
970 if (grepl(pattern = AN,
|
|
|
971 x = names(FTLwtmotifsFINAL[k]),
|
|
|
972 fixed = TRUE) == TRUE) {
|
|
|
973 outputmatrix <- as.character(Firstsubbackfreq[, m])
|
|
|
974 outputmatrix <- matrix(outputmatrix, nrow = 1)
|
|
|
975 #with that accession number, find a match in the subbackfreq file and save it here
|
|
|
976 FTLFinalMatrix<-rbind(FTLFinalMatrix,outputmatrix)
|
|
|
977 }
|
|
|
978 }
|
|
|
979 }
|
|
|
980 FTLFinalMatrix<-FTLFinalMatrix[!duplicated(FTLFinalMatrix),]
|
|
|
981
|
|
|
982 columnalheader<-c(rep(NA,36))
|
|
|
983 ITDFinalMatrix<-matrix(data =columnalheader,nrow = 1)
|
|
|
984
|
|
|
985 for (k in 1:length(ITDmotifsFINAL)) {
|
|
|
986 AN<-00000
|
|
|
987 #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
|
|
|
988 #destroyed immediately after use
|
|
|
989 for (m in 1:ncol(Thirdsubbackfreq)) {
|
|
|
990 AN <- as.character(Thirdsubbackfreq[1, m])
|
|
|
991 if (grepl(pattern = AN,
|
|
|
992 x = names(ITDmotifsFINAL[k]),
|
|
|
993 fixed = TRUE) == TRUE) {
|
|
|
994 outputmatrix <- as.character(Thirdsubbackfreq[, m])
|
|
|
995 outputmatrix <- matrix(outputmatrix, nrow = 1)
|
|
|
996 #with that accession number, find a match in the subbackfreq file and save it here
|
|
|
997 ITDFinalMatrix<-rbind(ITDFinalMatrix,outputmatrix)
|
|
|
998 }
|
|
|
999 }
|
|
|
1000 }
|
|
|
1001 ITDFinalMatrix<-ITDFinalMatrix[!duplicated(ITDFinalMatrix),]
|
|
|
1002
|
|
|
1003 columnalheader<-c(rep(NA,36))
|
|
|
1004 D835YFinalMatrix<-matrix(data =columnalheader,nrow = 1)
|
|
|
1005
|
|
|
1006 for (k in 1:length(D835YmotifsFINAL)) {
|
|
|
1007 #I don't remember why, but I felt it necessary to destroy the accession number multiple times to ensure it is
|
|
|
1008 #destroyed immediately after use
|
|
|
1009 for (m in 1:ncol(Secondsubbackfreq)) {
|
|
|
1010 AN <- as.character(Secondsubbackfreq[1, m])
|
|
|
1011 if (grepl(pattern = AN,
|
|
|
1012 x = names(D835YmotifsFINAL[k]),
|
|
|
1013 fixed = TRUE) == TRUE) {
|
|
|
1014 outputmatrix <- as.character(Secondsubbackfreq[, m])
|
|
|
1015 outputmatrix <- matrix(outputmatrix, nrow = 1)
|
|
|
1016 #with that accession number, find a match in the subbackfreq file and save it here
|
|
|
1017 D835YFinalMatrix<-rbind(D835YFinalMatrix,outputmatrix)
|
|
|
1018 }
|
|
|
1019 }
|
|
|
1020 }
|
|
|
1021 D835YFinalMatrix<-D835YFinalMatrix[!duplicated(D835YFinalMatrix),]
|
|
|
1022
|
|
|
1023 FTLoutputmatrix<-matrix(data=c(FTLwtmotifsFINAL,names(FTLwtmotifsFINAL)),ncol = 2)
|
|
|
1024
|
|
|
1025 #another fucking for loop
|
|
|
1026 FLTreference<-FTLoutputmatrix[,2]
|
|
|
1027
|
|
|
1028 FirstLine<-colnames(FirstSubstrateSet)
|
|
|
1029 FirstLine<-FirstLine[1:23]
|
|
|
1030 for (q in 1:nrow(FTLoutputmatrix)) {
|
|
|
1031 thismotif<-unlist(strsplit(FTLoutputmatrix[q,1],""))
|
|
|
1032 thisoutput<-c("","",FTLoutputmatrix[q,2],thismotif,"","","","","")
|
|
|
1033 FirstLine<-rbind(FirstLine,thisoutput)
|
|
|
1034 }
|
|
|
1035
|
|
|
1036
|
|
|
1037
|
|
|
1038 write.table(x=FirstLine,
|
|
|
1039 file=First_unshared_motifs_table,
|
|
|
1040 quote=FALSE, sep=",",
|
|
|
1041 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
1042
|
|
|
1043 columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1]))
|
|
|
1044 columnalheader<-matrix(columnalheader,nrow = 1)
|
|
|
1045
|
|
|
1046 # columnalheader<-rbind(columnalheader,FTLFinalMatrix)
|
|
|
1047
|
|
|
1048 write.table(x=columnalheader,
|
|
|
1049 file=First_unshared_subbackfreq,
|
|
|
1050 quote=FALSE, sep=",",
|
|
|
1051 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
1052
|
|
|
1053 write.table(x=FTLFinalMatrix[2:nrow(FTLFinalMatrix),],
|
|
|
1054 file=First_unshared_subbackfreq,
|
|
|
1055 quote=FALSE, sep=",",
|
|
|
1056 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
1057
|
|
|
1058 ############################################################################################################
|
|
|
1059
|
|
|
1060 D835Youtputmatrix<-matrix(data=c(D835YmotifsFINAL,names(D835YmotifsFINAL)),ncol = 2)
|
|
|
1061
|
|
|
1062 FLTreference<-D835Youtputmatrix[,2]
|
|
|
1063
|
|
|
1064 FirstLine<-colnames(FirstSubstrateSet)
|
|
|
1065 FirstLine<-FirstLine[1:23]
|
|
|
1066 for (q in 1:nrow(D835Youtputmatrix)) {
|
|
|
1067 thismotif<-unlist(strsplit(D835Youtputmatrix[q,1],""))
|
|
|
1068 thisoutput<-c("","",D835Youtputmatrix[q,2],thismotif,"","","","","")
|
|
|
1069 FirstLine<-rbind(FirstLine,thisoutput)
|
|
|
1070 }
|
|
|
1071
|
|
|
1072
|
|
|
1073
|
|
|
1074 write.table(x=FirstLine,
|
|
|
1075 file=Second_unshared_motifs_table,
|
|
|
1076 quote=FALSE, sep=",",
|
|
|
1077 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
1078
|
|
|
1079 columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1]))
|
|
|
1080 columnalheader<-matrix(columnalheader,nrow = 1)
|
|
|
1081
|
|
|
1082 # columnalheader<-rbind(columnalheader,D835YFinalMatrix)
|
|
|
1083
|
|
|
1084 write.table(x=columnalheader,
|
|
|
1085 file=Second_unshared_subbackfreq,
|
|
|
1086 quote=FALSE, sep=",",
|
|
|
1087 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
1088
|
|
|
1089 write.table(x=D835YFinalMatrix[2:nrow(D835YFinalMatrix),],
|
|
|
1090 file=Second_unshared_subbackfreq,
|
|
|
1091 quote=FALSE, sep=",",
|
|
|
1092 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
1093
|
|
|
1094 ############################################################################################################
|
|
|
1095
|
|
|
1096 ITDoutputmatrix<-matrix(data = c(ITDmotifsFINAL,names(ITDmotifsFINAL)),ncol = 2)
|
|
|
1097
|
|
|
1098 FLTreference<-ITDoutputmatrix[,2]
|
|
|
1099
|
|
|
1100 FirstLine<-colnames(FirstSubstrateSet)
|
|
|
1101 FirstLine<-FirstLine[1:23]
|
|
|
1102 for (q in 1:nrow(ITDoutputmatrix)) {
|
|
|
1103 thismotif<-unlist(strsplit(ITDoutputmatrix[q,1],""))
|
|
|
1104 thisoutput<-c("","",ITDoutputmatrix[q,2],thismotif,"","","","","")
|
|
|
1105 FirstLine<-rbind(FirstLine,thisoutput)
|
|
|
1106 }
|
|
|
1107
|
|
|
1108
|
|
|
1109 write.table(x=FirstLine,
|
|
|
1110 file=Third_unshared_motifs_table,
|
|
|
1111 quote=FALSE, sep=",",
|
|
|
1112 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
1113
|
|
|
1114 columnalheader<-c(as.character(Thirdsubbackfreq[1:36,1]))
|
|
|
1115 columnalheader<-matrix(columnalheader,nrow = 1)
|
|
|
1116
|
|
|
1117 # columnalheader<-rbind(columnalheader,ITDFinalMatrix)
|
|
|
1118
|
|
|
1119 write.table(x=columnalheader,
|
|
|
1120 file=Third_unshared_subbackfreq,
|
|
|
1121 quote=FALSE, sep=",",
|
|
|
1122 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
1123
|
|
|
1124 write.table(x=ITDFinalMatrix[2:nrow(ITDFinalMatrix),],
|
|
|
1125 file=Third_unshared_subbackfreq,
|
|
|
1126 quote=FALSE, sep=",",
|
|
|
1127 row.names=FALSE,col.names = FALSE, na="", append=TRUE)
|
|
|
1128
|
|
|
1129 }
|
