compareSteady {INSPEcT} | R Documentation |
This method compares two object of class INSPEcT in order to identify differential usage of synthesis, processing or degradation rates in two different steady-state conditions. The two INSPEcT objects must have been profiled with replicates in order to provide a statistical significance to the differences between their rates.
compareSteady(inspectIds, BPPARAM = bpparam()) ## S4 method for signature 'INSPEcT' compareSteady(inspectIds, BPPARAM = bpparam())
inspectIds |
An object of calss INSPEcT with two conditions |
BPPARAM |
Configuration for BiocParallel parallelization. By default is set to bpparam() |
An object of class INSPEcT_diffsteady which contains both the absolute
quantification of the rates as well as the comparison with the statistical significance
associated for each gene and rate. (See INSPEcT_diffsteady-class
)
if( Sys.info()["sysname"] != "Windows" ) { data('allcounts', package='INSPEcT') data('featureWidths', package='INSPEcT') data('libsizes', package='INSPEcT') nascentCounts<-allcounts$nascent matureCounts<-allcounts$mature conditions<-letters[1:11] expDes<-rep(conditions,3) tL<-1/6 nasExp_DESeq2<-quantifyExpressionsFromTrCounts( allcounts=nascentCounts ,libsize=nascentLS ,exonsWidths=exWdths ,intronsWidths=intWdths ,experimentalDesign=expDes) matExp_DESeq2<-quantifyExpressionsFromTrCounts( allcounts=matureCounts ,libsize=totalLS ,exonsWidths=exWdths ,intronsWidths=intWdths ,experimentalDesign=expDes) nasFullObj <- newINSPEcT( tpts=conditions ,labeling_time=tL ,nascentExpressions=nasExp_DESeq2 ,matureExpressions=matExp_DESeq2) diffrates = compareSteady(nasFullObj[,c(1,11)]) }