processingDelay: Classify genes as delayed by the processing using the delta...

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

Description

These functions calculates the tau and delta metrics for all genes with introns and exons in an oblect of class INSPEcT. If the INSPEcT dataset was obtained with nascent RNA the metrics are caluclated using RNA dynamics and solving numerically the system of equations. If the INSPEcT dataset was obtained without nascent RNA the metrics are approximated using premature and mature levels.

Usage

processingDelay(
  inspectIds,
  tauThreshold = 1.2,
  deltaThreshold = 1,
  silent = TRUE
)

calculateDelta(inspectIds, silent = FALSE)

calculateTau(inspectIds, silent = FALSE)

## S4 method for signature 'INSPEcT'
processingDelay(
  inspectIds,
  tauThreshold = 1.2,
  deltaThreshold = 1,
  silent = TRUE
)

## S4 method for signature 'INSPEcT'
calculateTau(inspectIds, silent = FALSE)

## S4 method for signature 'INSPEcT'
calculateDelta(inspectIds, silent = FALSE)

Arguments

inspectIds	An object of class INSPEcT.
tauThreshold	A numeric representing the tau threshold to define a gene affected by processing. Default: 1.2
deltaThreshold	A numeric representing the delta threshold to define a gene affected by processing. Default: 1.0
silent	A logical indicating whether informaiton about the procedure should be printed or not.

Examples

data('allcounts', package='INSPEcT')
data('featureWidths', package='INSPEcT')
data('libsizes', package='INSPEcT')

nascentCounts<-allcounts$nascent
matureCounts<-allcounts$mature
conditions<-c(0,1/6,1/3,1/2,1,1.5,2,4,8,12,16)
expDes<-rep(conditions,3)
tL <- 1/6

nasExp_DESeq2<-quantifyExpressionsFromTrCounts(
      allcounts=matureCounts
      ,libsize=totalLS
      ,exonsWidths=exWdths
      ,intronsWidths=intWdths
      ,experimentalDesign=expDes)

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

matureInspObj <- newINSPEcT(
      tpts=conditions
      ,labeling_time=tL
      ,nascentExpressions=nasExp_DESeq2
      ,matureExpressions=matExp_DESeq2)

procDelay<- processingDelay(inspectIds=matureInspObj
      ,tauThreshold=1.2
      ,deltaThreshold=1.0)

head(procDelay)
table(procDelay)

head(calculateTau(matureInspObj))

head(calculateDelta(matureInspObj))

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