Mercurial > repos > mmonsoor > probmetab
diff lib.r @ 4:52b222a626b0 draft default tip
planemo upload commit 00684d80f032fee5bd1cb86e05a477fcdcb1c3fc
| author | lecorguille |
|---|---|
| date | Fri, 07 Apr 2017 09:11:22 -0400 |
| parents | abcfa1648b66 |
| children |
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--- a/lib.r Fri Apr 07 07:14:12 2017 -0400 +++ b/lib.r Fri Apr 07 09:11:22 2017 -0400 @@ -122,7 +122,7 @@ ansConn = export.class.table(conn, reactionM, ionAnnot, DB=DB,html=listArguments[["html"]],filename="AnalysisExample",prob=listArguments[["prob"]]) if(listArguments[["html"]]){ #Zip the EICS plot - system(paste('zip -r "Analysis_Report.zip" "AnalysisExample_fig"')) + system(paste('zip -rq "Analysis_Report.zip" "AnalysisExample_fig"')) } # calculate the correlations and partial correlations and cross reference then with reactions @@ -148,10 +148,10 @@ write.table(variableM, sep="\t", quote=FALSE, row.names=FALSE, file="variableMetadata.tsv") } else if (listArguments[["mode_acquisition"]]=="two") { #Retrocompatibility with previous annotateDiffreport variableMetadata dataframe (must replace mzmed column by mz, and rtmed by rt) - names(variableMetadataP)[names(variableMetadata)=="mzmed"] <- "mz" - names(variableMetadataP)[names(variableMetadata)=="rtmed"] <- "rt" - names(variableMetadataN)[names(variableMetadata)=="mzmed"] <- "mz" - names(variableMetadataN)[names(variableMetadata)=="rtmed"] <- "rt" + names(variableMetadataP)[names(variableMetadataP)=="mzmed"] <- "mz" + names(variableMetadataP)[names(variableMetadataP)=="rtmed"] <- "rt" + names(variableMetadataN)[names(variableMetadataN)=="mzmed"] <- "mz" + names(variableMetadataN)[names(variableMetadataN)=="rtmed"] <- "rt" variableMP=merge_probmetab(variableMetadataP, ansConn) write.table(variableMP, sep="\t", quote=FALSE, row.names=FALSE, file="variableMetadata_Positive.tsv") variableMN=merge_probmetab(variableMetadataN, ansConn)