INSPEcT_diffsteady-class {INSPEcT} | R Documentation |
INSPEcT_diffsteady is a class able to store the results of the comparisons between two steady states.
An object of class INSPEcT_diffsteady is created with the method "compareSteady" applied on
two "INSPEcT" objects (see compareSteady
).
synthesis(object) processing(object) degradation(object) ## S4 method for signature 'INSPEcT_diffsteady' show(object) ## S4 method for signature 'INSPEcT_diffsteady' synthesis(object) ## S4 method for signature 'INSPEcT_diffsteady' processing(object) ## S4 method for signature 'INSPEcT_diffsteady' degradation(object) ## S4 method for signature 'INSPEcT_diffsteady' featureNames(object)
object |
An object of class INSPEcT_model |
Methods associated to the class INSPEcT_diffsteady are:
synthesis: Accessor to the synthesis rates and their comparisons.
degradation: Accessor to the degradation rates and their comparisons.
processing: Accessor to the processing rates and their comparisons.
plotMA: visualization fuction for rates comparisons, see plotMA
Method show for objects of class INSPEcT_model returns the number of the genes that have been modeled
synthesis
A data.frame which contains both input data and comparisons results regarding synthesis rates
degradation
A data.frame which contains both input data and comparisons results regarding degradation rates
processing
A data.frame which contains both input data and comparisons results regarding processing rates
modeling_res
A data.frame which contains modeling results
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)]) head(synthesis(diffrates)) } if( Sys.info()["sysname"] != "Windows" ) { head(processing(diffrates)) } if( Sys.info()["sysname"] != "Windows" ) { head(degradation(diffrates)) } if( Sys.info()["sysname"] != "Windows" ) { featureNames(diffrates) }