compareSteadyNoNascent: Identify post-transcriptionally regulated genes from an...

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

Description

This function compare exons and introns expression level matrices, from two up to an arbitrary number of samples, in order to identify genes which are oddly regluated, compared to an expected standard behaviour, from the post transcriptional point of view.

Usage

compareSteadyNoNascent(
  inspectIds,
  expressionThreshold = 0.25,
  log2FCThreshold = 2,
  trivialAngle = NaN,
  returnNormScores = FALSE,
  referenceCondition = "median"
)

## S4 method for signature 'INSPEcT_steadyNoNascent'
compareSteadyNoNascent(
  inspectIds,
  expressionThreshold = 0.25,
  log2FCThreshold = 2,
  trivialAngle = NaN,
  returnNormScores = FALSE,
  referenceCondition = "median"
)

Arguments

inspectIds	An object of class INSPEcT_steadyNoNascent
expressionThreshold	A parameter which sets how many log2 fold changes of distance from the median behaviour are imputable to noise.
log2FCThreshold	A parameter which sets the log2 fold change distance from the median behaviour that is imputable to noise.
trivialAngle	A numeric between 0 and 90 to define the standard behavior, if NaN (default) it is computed internally from the data.
returnNormScores	A logical, if TRUE returned the deviations from the standard behavior normalized by the sd.
referenceCondition	The label of the condition to use as reference, if NaN (default) the medians are used.

Examples

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)

matExp_DESeq2<-quantifyExpressionsFromTrCounts(
      allcounts=matureCounts
      ,libsize=totalLS
      ,exonsWidths=exWdths
      ,intronsWidths=intWdths
      ,experimentalDesign=expDes)

matureInspObj <- newINSPEcT(tpts=conditions,matureExpressions=matExp_DESeq2)

matureInspObj<-compareSteadyNoNascent(inspectIds=matureInspObj
								 ,expressionThreshold=0.25
							 ,log2FCThreshold=.5)
regGenes <- PTreg(matureInspObj)
head(regGenes)
table(regGenes)

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