Mercurial > repos > mmonsoor > probmetab

comparison lib.r @ 9:fe21deb6b625 draft

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planemo upload commit 4119e0f73e028bf420e5bdec2d95a4621ebbbcaf
author lecorguille
date Fri, 07 Apr 2017 07:56:16 -0400
parents 66fe5a2237f3
children 2964f7864315
comparison
equal deleted inserted replaced
8:66fe5a2237f3 9:fe21deb6b625
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 }