Mercurial > repos > tomnl > assess_purity_msms

annotate create_sqlite_db.R @ 28:fa5838760aee draft default tip

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875
author tomnl
date Wed, 18 Jul 2018 05:54:55 -0400
parents 7bff866f72b5
children
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1 library(msPurity)
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2 library(optparse)
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3 library(xcms)
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4 library(CAMERA)
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5 print(sessionInfo())
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6 print('CREATING DATABASE')
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9 xset_pa_filename_fix <- function(opt, pa, xset){
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10 print(xset@filepaths)
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12 if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){
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13 # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables
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14 # needs to be done due to Galaxy moving the files around and screwing up any links to files
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16 filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]])
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17 filepaths <- filepaths[filepaths != ""]
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18 new_names <- basename(filepaths)
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20 galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
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21 galaxy_names <- galaxy_names[galaxy_names != ""]
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23 nsave <- names(pa@fileList)
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24 old_filenames <- basename(pa@fileList)
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25 pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)]
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26 names(pa@fileList) <- nsave
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28 pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)])
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29 pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)])
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30 }
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33 if(!all(basename(pa@fileList)==basename(xset@filepaths))){
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34 if(!all(names(pa@fileList)==basename(xset@filepaths))){
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35 print('FILELISTS DO NOT MATCH')
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36 message('FILELISTS DO NOT MATCH')
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37 quit(status = 1)
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38 }else{
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39 xset@filepaths <- unname(pa@fileList)
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40 }
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41 }
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44 print(xset@phenoData)
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45 print(xset@filepaths)
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47 return(list(pa, xset))
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48 }
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53 option_list <- list(
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54 make_option(c("-o", "--out_dir"), type="character"),
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55 make_option("--pa", type="character"),
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56 make_option("--xset_xa", type="character"),
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57 make_option("--xcms_camera_option", type="character"),
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58 make_option("--eic", action="store_true"),
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59 make_option("--cores", default=4),
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60 make_option("--mzML_files", type="character"),
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61 make_option("--galaxy_names", type="character"),
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62 make_option("--grp_peaklist", type="character"),
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63 make_option("--db_name", type="character", default='lcms_data.sqlite'),
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64 make_option("--raw_rt_columns", action="store_true"),
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65 make_option("--metfrag_result", type="character"),
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66 make_option("--sirius_csifingerid_result", type="character"),
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67 make_option("--probmetab_result", type="character")
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68 )
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71 # store options
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72 opt<- parse_args(OptionParser(option_list=option_list))
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74 loadRData <- function(rdata_path, name){
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75 #loads an RData file, and returns the named xset object if it is there
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76 load(rdata_path)
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77 return(get(ls()[ls() == name]))
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78 }
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80 print(paste('pa', opt$pa))
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81 print(opt$xset)
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83 print(opt$xcms_camera_option)
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84 # Requires
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85 pa <- loadRData(opt$pa, 'pa')
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88 print(pa@fileList)
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91 if (opt$xcms_camera_option=='xcms'){
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92 xset <- loadRData(opt$xset, 'xset')
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93 fix <- xset_pa_filename_fix(opt, pa, xset)
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94 pa <- fix[[1]]
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95 xset <- fix[[2]]
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96 xa <- NULL
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97 }else{
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98
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99 xa <- loadRData(opt$xset, 'xa')
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100 fix <- xset_pa_filename_fix(opt, pa, xa@xcmsSet)
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101 pa <- fix[[1]]
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102 xa@xcmsSet <- fix[[2]]
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103 xset <- NULL
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104 }
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105
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106
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107
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108
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109
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110 if(is.null(opt$grp_peaklist)){
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111 grp_peaklist = NA
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112 }else{
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113 grp_peaklist = opt$grp_peaklist
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114 }
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115
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116
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117
1
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118 db_pth <- msPurity::create_database(pa, xset=xset, xsa=xa, out_dir=opt$out_dir,
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119 grp_peaklist=grp_peaklist, db_name=opt$db_name)
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120
14
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121 print(db_pth)
1
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122
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123 if (!is.null(opt$eic)){
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124 if (is.null(opt$raw_rt_columns)){
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125 rtrawColumns <- FALSE
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126 }else{
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127 rtrawColumns <- TRUE
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128 }
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129 if (is.null(xset)){
19
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130 xset <- xa@xcmsSet
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131 }
14
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132 # previous check should have matched filelists together
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133 xset@filepaths <- unname(pa@fileList)
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134
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135 # Saves the EICS into the previously created database
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136 px <- msPurity::purityX(xset, saveEIC = TRUE,
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137 cores=1, sqlitePth=db_pth,
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138 rtrawColumns = rtrawColumns)
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139 }
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140
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141 con <- DBI::dbConnect(RSQLite::SQLite(), db_pth)
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142
22
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143 add_extra_table_elucidation <- function(name, pth, db_con){
20
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144 if (is.null(pth)){
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145 return(0)
22
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146 }
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147
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148
21
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149 DBI::dbWriteTable(conn=db_con, name=name, value=pth, sep='\t', header=T)
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150
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151
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152 }
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153
21
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154 write_to_table <- function(df, db_con, name, append){
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155
20
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156 df <- df[!df$UID=='UID',]
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157 print(filter_Score)
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158 print(filter_Rank)
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159 print('filter rank and score')
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160
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161
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162 # get peakid, an scan id
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163 df_ids <- stringr::str_split_fixed(df$UID, '-', 3)
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164 colnames(df_ids) <- c('grp_id', 'file_id', 'pid')
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165 df <- cbind(df_ids, df)
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166 DBI::dbWriteTable(db_con, name=name, value=df, row.names=FALSE, append=append)
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167 }
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168
22
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169 add_probmetab <- function(pth, xset, con){
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170 if (!is.null(pth)){
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171
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172 df <- read.table(pth, header = TRUE, sep='\t', stringsAsFactors = FALSE, comment.char = "")
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173 df$grp_id <- match(df$name, xcms::groupnames(xset))
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174 start <- T
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175 for (i in 1:nrow(df)){
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176
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177 x <- df[i,]
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178
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179
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180 if(is.na(x$proba) | x$proba =='NA'){
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181
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182 next
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183 }
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184
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185 mpc <- stringr::str_split(x$mpc, ';')
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186 proba <- stringr::str_split(x$proba, ';')
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187
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188 for (j in 1:length(mpc[[1]])){
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189
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190 row <- c(x$grp_id, x$propmz, mpc[[1]][j], proba[[1]][j])
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191
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192 if (start){
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193 df_out <- data.frame(t(row), stringsAsFactors=F)
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194 start <- F
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195 }else{
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196 df_out <- data.frame(rbind(df_out, row), stringsAsFactors=F)
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197 }
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198 print(df_out)
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199
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200 }
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201
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202 }
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203
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204 colnames(df_out) <- c('grp_id', 'propmz', 'mpc', 'proba')
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205 DBI::dbWriteTable(con, name='probmetab_results', value=df_out, row.names=FALSE)
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206
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207 }
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208
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209
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210 }
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211
23
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212 add_extra_table_elucidation('metfrag_results', opt$metfrag_result, con)
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213 add_extra_table_elucidation('sirius_csifingerid_results', opt$sirius_csifingerid_result, con)
22
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214
13
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215
21
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216 if (is.null(xset)){
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217 DBI::dbWriteTable(con, name='xset_classes', value=xa@xcmsSet@phenoData, row.names=TRUE)
24
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218 add_probmetab(opt$probmetab_result, xa@xcmsSet, con)
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219 }else{
1
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220
21
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221 DBI::dbWriteTable(con, name='xset_classes', value=xset@phenoData, row.names=TRUE)
22
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222 add_probmetab(opt$probmetab_result, xset, con)
1
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223
21
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224 }
1
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225
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226 cmd <- paste('SELECT cpg.grpid, cpg.mz, cpg.mzmin, cpg.mzmax, cpg.rt, cpg.rtmin, cpg.rtmax, c_peaks.cid, ',
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227 'c_peaks.mzmin AS c_peak_mzmin, c_peaks.mzmax AS c_peak_mzmax, ',
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228 'c_peaks.rtmin AS c_peak_rtmin, c_peaks.rtmax AS c_peak_rtmax, s_peak_meta.*, fileinfo.filename, fileinfo.nm_save ',
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229 'FROM c_peak_groups AS cpg ',
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230 'LEFT JOIN c_peak_X_c_peak_group AS cXg ON cXg.grpid=cpg.grpid ',
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231 'LEFT JOIN c_peaks on c_peaks.cid=cXg.cid ',
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232 'LEFT JOIN c_peak_X_s_peak_meta AS cXs ON cXs.cid=c_peaks.cid ',
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233 'LEFT JOIN s_peak_meta ON cXs.pid=s_peak_meta.pid ',
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234 'LEFT JOIN fileinfo ON s_peak_meta.fileid=fileinfo.fileid')
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235
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236 print(cmd)
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237 cpeakgroup_msms <- DBI::dbGetQuery(con, cmd)
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238
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239 write.table(cpeakgroup_msms, file.path(opt$out_dir, 'cpeakgroup_msms.tsv'), row.names=FALSE, sep='\t')