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comparison lib.r @ 4:52b222a626b0 draft default tip

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planemo upload commit 00684d80f032fee5bd1cb86e05a477fcdcb1c3fc
author lecorguille
date Fri, 07 Apr 2017 09:11:22 -0400
parents abcfa1648b66
children
comparison
equal deleted inserted replaced
3:abcfa1648b66 4:52b222a626b0
120 y = 1:nrow(wl$wm) 120 y = 1:nrow(wl$wm)
121 conn = gibbs.samp(x, y, 5000, w, wl$wm) 121 conn = gibbs.samp(x, y, 5000, w, wl$wm)
122 ansConn = export.class.table(conn, reactionM, ionAnnot, DB=DB,html=listArguments[["html"]],filename="AnalysisExample",prob=listArguments[["prob"]]) 122 ansConn = export.class.table(conn, reactionM, ionAnnot, DB=DB,html=listArguments[["html"]],filename="AnalysisExample",prob=listArguments[["prob"]])
123 if(listArguments[["html"]]){ 123 if(listArguments[["html"]]){
124 #Zip the EICS plot 124 #Zip the EICS plot
125 system(paste('zip -r "Analysis_Report.zip" "AnalysisExample_fig"')) 125 system(paste('zip -rq "Analysis_Report.zip" "AnalysisExample_fig"'))
126 } 126 }
127 127
128 # calculate the correlations and partial correlations and cross reference then with reactions 128 # calculate the correlations and partial correlations and cross reference then with reactions
129 mw=which(w==1,arr.ind=TRUE) 129 mw=which(w==1,arr.ind=TRUE)
130 #reac2cor function : Use the intensity of putative molecules in repeated samples to calculate correlations and partial 130 #reac2cor function : Use the intensity of putative molecules in repeated samples to calculate correlations and partial
146 names(variableMetadata)[names(variableMetadata)=="rtmed"] <- "rt" 146 names(variableMetadata)[names(variableMetadata)=="rtmed"] <- "rt"
147 variableM=merge_probmetab(variableMetadata, ansConn) 147 variableM=merge_probmetab(variableMetadata, ansConn)
148 write.table(variableM, sep="\t", quote=FALSE, row.names=FALSE, file="variableMetadata.tsv") 148 write.table(variableM, sep="\t", quote=FALSE, row.names=FALSE, file="variableMetadata.tsv")
149 } else if (listArguments[["mode_acquisition"]]=="two") { 149 } else if (listArguments[["mode_acquisition"]]=="two") {
150 #Retrocompatibility with previous annotateDiffreport variableMetadata dataframe (must replace mzmed column by mz, and rtmed by rt) 150 #Retrocompatibility with previous annotateDiffreport variableMetadata dataframe (must replace mzmed column by mz, and rtmed by rt)
151 names(variableMetadataP)[names(variableMetadata)=="mzmed"] <- "mz" 151 names(variableMetadataP)[names(variableMetadataP)=="mzmed"] <- "mz"
152 names(variableMetadataP)[names(variableMetadata)=="rtmed"] <- "rt" 152 names(variableMetadataP)[names(variableMetadataP)=="rtmed"] <- "rt"
153 names(variableMetadataN)[names(variableMetadata)=="mzmed"] <- "mz" 153 names(variableMetadataN)[names(variableMetadataN)=="mzmed"] <- "mz"
154 names(variableMetadataN)[names(variableMetadata)=="rtmed"] <- "rt" 154 names(variableMetadataN)[names(variableMetadataN)=="rtmed"] <- "rt"
155 variableMP=merge_probmetab(variableMetadataP, ansConn) 155 variableMP=merge_probmetab(variableMetadataP, ansConn)
156 write.table(variableMP, sep="\t", quote=FALSE, row.names=FALSE, file="variableMetadata_Positive.tsv") 156 write.table(variableMP, sep="\t", quote=FALSE, row.names=FALSE, file="variableMetadata_Positive.tsv")
157 variableMN=merge_probmetab(variableMetadataN, ansConn) 157 variableMN=merge_probmetab(variableMetadataN, ansConn)
158 write.table(variableMN, sep="\t", quote=FALSE, row.names=FALSE, file="variableMetadata_Negative.tsv") 158 write.table(variableMN, sep="\t", quote=FALSE, row.names=FALSE, file="variableMetadata_Negative.tsv")
159 } 159 }