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comparison lib.r @ 8:66fe5a2237f3 draft

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planemo upload commit c897279aa8cae0a4ad889bb05b143f32d2b6d712
author lecorguille
date Fri, 07 Apr 2017 06:55:52 -0400
parents a1b528cba999
children fe21deb6b625
comparison
equal deleted inserted replaced
7:cbf292c32002 8:66fe5a2237f3
48 # load(listArguments[["xsetNnofill"]]) 48 # load(listArguments[["xsetNnofill"]])
49 # xsetNnofill=xset 49 # xsetNnofill=xset
50 #} 50 #}
51 # include CAMERA non-annotated compounds, and snr retrieval 51 # include CAMERA non-annotated compounds, and snr retrieval
52 # comb 2+ - used on Table 1 52 # comb 2+ - used on Table 1
53 ionAnnotP2plus = get.annot(axP, allowMiss=listArguments[["allowMiss"]], xset=xsetPnofill,toexclude=listArguments[["toexclude"]]) 53 ionAnnotP2plus = get.annot(xaP, allowMiss=listArguments[["allowMiss"]], xset=xsetPnofill,toexclude=listArguments[["toexclude"]])
54 ionAnnotN2plus = get.annot(axN, polarity="negative", allowMiss=listArguments[["allowMiss"]], xset=xsetNnofill,toexclude=listArguments[["toexclude"]]) 54 ionAnnotN2plus = get.annot(xaN, polarity="negative", allowMiss=listArguments[["allowMiss"]], xset=xsetNnofill,toexclude=listArguments[["toexclude"]])
55 ionAnnot = combineMolIon(ionAnnotP2plus, ionAnnotN2plus) 55 ionAnnot = combineMolIon(ionAnnotP2plus, ionAnnotN2plus)
56 print(sum(ionAnnot$molIon[,3]==1)) 56 print(sum(ionAnnot$molIon[,3]==1))
57 print(sum(ionAnnot$molIon[,3]==0)) 57 print(sum(ionAnnot$molIon[,3]==0))
58 write.table(ionAnnot[1], sep="\t", quote=FALSE, row.names=FALSE, file="CombineMolIon.tsv") 58 write.table(ionAnnot[1], sep="\t", quote=FALSE, row.names=FALSE, file="CombineMolIon.tsv")
59 #Merge variableMetadata Negative and positive acquisitions mode 59 #Merge variableMetadata Negative and positive acquisitions mode