CalGIFCalculatetheglobalin3uencefactorGIF DescriptionCalGIFisanattempttocalculatetheGIFscorewhichisusedtodistinguishthenonequivalenceofgenein3uencedbybothinternaleffectofpathwaysandcrosstalkb ID: 854521
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1 2CalGIFIndex10 CalGIFCalculatetheglobali
2CalGIFIndex10 CalGIFCalculatetheglobalinuencefactor(GIF) DescriptionCalGIFisanattempttocalculatetheGIFscorewhichisusedtodistinguishthenon-equivalenceofgeneinuencedbybothinternaleffectofpathwaysandcrosstalkbetweenpathways.Therandomwalkwithrestart(RWR)algorithmwasusedtoevaluatetheGIFbyintegratingtheglobalnetworktopologyandthecorrelationofgenewithphenotype.UsageCalGIF(dataset,class.labels)ArgumentsdatasetAdataframeofgeneexpressiondatawhoserstcolumnaregenessymbolsandwhosenamesaresamples.class.labelsAvectorofbinarylabels.Thevectorisusedtodistinguishtheclassofpheno-type.DetailsWhenusersinputinterestinggeneexpressiondataandthevectorofbinarylabels(cla
2 sslabels),thefunctioncancalculatetheGIFv
sslabels),thefunctioncancalculatetheGIFvaluesforallgenesintheglobalgene-genenetworkconstructedbasedontherelationshipsofgenesextractedfrompathwaydatabase.Theargumentdatasetisgeneexpressiondatasetstoredinadataframe.Therstcolumnofthedataframearegenesymbolsandthenamesofthedataframearesamplesnames.ValueAvector.EachelementistheGIFscoreandwhosenamecorrespondtogenesymbolinthegeneexpressiondata.Author(s)JunweiHan&#xhanj;&#xunwe;&#xi198;@16;.co;&#xm000;YanjunXu&#xtong;&#xhua6;@1;c.c;&#xom00;HaixiuYang&#xyang;&#x-]TJ;&#x 0 -;.9;U T; [0;haixiu@ems.hrbmu.edu.cnChunquanLi&#xlcqb;&#xio@y; hoo;&#x.com;&#x.cn0;andXiaLi&#xlixi; @hr;&#
3 xbmu.;íu.;n00; 4getclass.labelsD
xbmu.;íu.;n00; 4getclass.labelsDetailsTheenvironmentvariableincludesthevariabledataset,class.labelsetc.Author(s)JunweiHan&#xhanj;&#xunwe;&#xi198;@16;.co;&#xm000;YanjunXu&#xtong;&#xhua6;@1;c.c;&#xom00;HaixiuYang&#xyang;&#x-]TJ;&#x 0 -;.9;U T; [0;haixiu@ems.hrbmu.edu.cnChunquanLi&#xlcqb;&#xio@y; hoo;&#x.com;&#x.cn0;andXiaLi&#xlixi; @hr; mu.;íu.;n00; getclass.labelsGetthelabelsofexampledataset DescriptionGetthelabelsofexampledataset.Usagegetclass.labels()DetailsThelabelsoftheexampledataareobtainedfromtheenvironmentvariableExampleData.ValueAcharactervectorofclasslabels.Author(s)JunweiHan&#xhanj;&#xunwe;&#x
4 i198;@16;.co;&#xm000;YanjunXu&#x
i198;@16;.co;&#xm000;YanjunXu&#xtong;&#xhua6;@1;c.c;&#xom00;HaixiuYang&#xyang;&#x-]TJ;&#x 0 -;.9;U T; [0;haixiu@ems.hrbmu.edu.cnChunquanLi&#xlcqb;&#xio@y; hoo;&#x.com;&#x.cn0;andXiaLi&#xlixi; @hr; mu.;íu.;n00;SeeAlsogetdatasetExamples##Notrun:#obtainthelabelsoftheexampledatasetclass.labels()##End(Notrun) 6PAGI.Main PAGI.MainAnovelpathwayidenticationapproachbasedonglobalinuencefromboththeinternaleffectofpathwaysandcrosstalkbetweenpath-ways DescriptionPAGI.Mainisanattempttoidentifydysregulatedpathways,whichareinuencedbyboththeinter-naleffectofpathwaysandcrosstalkbetweenpathways,integratingpathwaytopo
5 logicalinformationanddifferencesbetweent
logicalinformationanddifferencesbetweentwobiologicalphenotypes.UsagePAGI.Main(dataset,class.labels,nperm=100,p.val.threshold=-1,FDR.threshold=0.01,gs.size.threshold.min=25,gs.size.threshold.max=500)ArgumentsdatasetAdataframeofgeneexpressiondatawhoserstcolumnaregenessymbolsandwhosenamesaresamples.class.labelsAvectorofbinarylabels.Thevectorisusedtodistinguishtheclassofpheno-type.npermAninteger.Thenumberofrandompermutations.Thedefaultvalueis100.p.val.thresholdAvalue.ThesignicancethresholdofNOMp-valueforpathwayswhosedetailresultsofpathwaystobepresented.Thedefaultvalueis-1,whichmeansnothreshold.FDR.thresholdAvalue.ThesignicancethresholdofFDRq-valuef
6 orpathwayswhosedetailresultsofpathwaysto
orpathwayswhosedetailresultsofpathwaystobepresented.Thedefaultvalueis0.01.gs.size.threshold.minAninteger.Theminimumsize(ingenes)forpathwaystobeconsidered.Thedefaultvalueis25.gs.size.threshold.maxAninteger.Themaximumsize(ingenes)forpathwaystobeconsidered.Thedefaultvalueis500.DetailsWhenusersinputinterestinggeneexpressiondataandthevectorofbinarylabels(classlabels),thefunctioncanidentifydysregulatedpathwaysmainlythrough:(1)Mappinggeneswiththeabsolutet-scoremorethan0totheglobalgraphreconstructedbasedontherelationshipsofgenesextractedfromeachpathwayinKEGGdatabaseandtheoverlappedgenesbetweenpathways;(2)Wede-nedaglobalinuencefactor(GIF)todistinguishthenon
7 -equivalenceofgeneinuencedbybothinte
-equivalenceofgeneinuencedbybothinternaleffectofpathwaysandcrosstalkbetweenpathwaysintheglobalnetwork.Therandomwalkwithrestart(RWR)algorithmwasusedtoevaluatetheGIFbyintegratingtheglobalnetworktopologyandthecorrelationofgenewithphenotype;(3)Weusedcumulativedistributionfunctions 8PAGI.Main#printthesummaryresultsofpathwaystoscreenresult[[1]][1:10,]#Theresultisadataframe.TherowsofthedataframearerankedbythevaluesofFalse#discoveryrate(FDR).Eachrowoftheresult(dataframe)isapathway.Itcolumnsinclude#"PathwayName","SIZE","PathwayID","PathwayScore","NOMp-val","FDRq-val","Tag#percentage","Genepercentage","Signalstrength".Theycorrespondtopathwaynames,#thenumberofgen
8 eswhichweremappedtothepathwayfromgeneexp
eswhichweremappedtothepathwayfromgeneexpressionprofiles,pathwayID,#thescoresofpathway,thenominalp-valuesofthepathways,theFDRvalues,thepercentof#genesetbeforerunningenrichmentpeak,thepercentofgenelistbeforerunningenrichmentpeak,#enrichmentsignalstrength.#printthedetailresultsofpathwaystoscreenresult[[2]][1:5]#Theresultisalist.Eachelementofthelistisadataframewhcihpresentthedetailresultsof#genesinthepathwaywithFDR.threshold0.01.Eachrowsofthedataframerepresentsagene.#Itscolumnsinclude"Genenumberinthe(sorted)pathway","genesymbolfromthegeneexpressdata",#"locationofthegeneinthesortedgenelist","theT-scoreofgenebetweentwobiologicalstates",#"globalinfluenceimpactor"
9 ,"ifthegenecontributetothescoreofpathway
,"ifthegenecontributetothescoreofpathway".#writethesummaryresultsofpathwaystotabdelimitedfile.write.table(result[[1]],file="SUMMARYRESULTS.txt",quote=F,row.names=F,sep="\t")#writethedetailresultsofgenesforeachpathwaywithFDR.threshold0.01totabdelimitedfile.for(iin1:length(result[[2]])){gene.reportfilenamepaste(names(result[[2]][i]),".txt",sep="",collapse="")write.table(gene.report,file=filename,quote=F,row.names=F,sep="\t")}#example2#getexampledatadataset((())header=T,sep="\t","\"")class.labels(((()"/localdata/class.labels.txt",sep=""),quote="\"",stringsAsFactors=FALSE)[1,])#identifydysregulatedpathwaysresult(=100,p.val.threshold=-1,FDR.threshold=0.01,gs.si
10 ze.threshold.min=25,gs.size.threshold.ma
ze.threshold.min=25,gs.size.threshold.max=500)#printthesummaryresultsofpathwaystoscreenresult[[1]][1:10,]#Theresultisadataframe.TherowsofthedataframearerankedbythevaluesofFalse#discoveryrate(FDR).Eachrowoftheresult(dataframe)isapathway.Itcolumnsinclude#"PathwayName","SIZE","PathwayID","PathwayScore","NOMp-val","FDRq-val","Tag#percentage","Genepercentage","Signalstrength".Theycorrespondtopathwaynames,#thenumberofgeneswhichweremappedtothepathwayfromgeneexpressionprofiles,pathwayID,#thescoresofpathway,thenominalp-valuesofthepathways,theFDRvalues,thepercentof#genesetbeforerunningenrichmentpeak,thepercentofgenelistbeforerunningenrichmentpeak,#enrichmentsignalst