INSPEcT_diffsteady-class: An S4 class to represent comparisons between two steady-state...

In ste-depo/INSPEcT: Modeling RNA synthesis, processing and degradation with RNA-seq data

Description

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).

Usage

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)

Arguments

object

An object of class INSPEcT_model

Details

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

Value

Method show for objects of class INSPEcT_model returns the number of the genes that have been modeled

Slots

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

Examples

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)
}

ste-depo/INSPEcT documentation built on Oct. 3, 2020, 9:14 p.m.