newINSPEcT: Create a new INSPEcT object

Description Usage Arguments Value Examples

View source: R/newINSPEcT-functions.R

Description

The function newINSPEcT creates a new instance of the class INSPEcT provided the experimental time points, expression data (like RPKMs) of mature and eventually nascent RNA. For the nascent analysis, it is also requires a collecting time and the scaling factor to normalize the nascent RNA-seq libraries. This latter parameter can also be calculated by the function itself if both exonic and intronic expression data are provided; otherwise it must be given as an input and it is essential to guarantee the robustness of the analysis.

Usage

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newINSPEcT(tpts, labeling_time = NULL, nascentExpressions = NULL,
  matureExpressions, BPPARAM = bpparam(), totalMedianNorm = TRUE,
  labeledMedianNorm = FALSE, totalSF = NULL, labeledSF = NULL,
  totalQuantileNorm = FALSE, labeledQuantileNorm = FALSE,
  simulatedData = FALSE, degDuringPulse = FALSE, Dmin = 1e-06,
  Dmax = 10, genesFilter = TRUE)

Arguments

tpts

A vector of time points, one for each sample

labeling_time

A number, lenght of the Nascent pulse

nascentExpressions

A list which contains exons and introns expression matrices and variances for the nascent RNA

matureExpressions

A list which contains exons and introns expression matrices and variances for the mature RNA

BPPARAM

Configuration for BiocParallel parallelization. By default is set to bpparam()

totalMedianNorm

A logical to perform median normalization over total RNA exons rpkms, it will apply also on introns

labeledMedianNorm

A logical to perform median normalization over Nascent RNA exons rpkms, it will apply also on introns

totalSF

A vector storing user defined normalization scale over Total RNA exons and introns rpkms

labeledSF

A vector storing user defined normalization scale over Nascent RNA exons and introns rpkms

totalQuantileNorm

A logical to perform to perform median normalization over total RNA exons rpkms, it will apply also on introns

labeledQuantileNorm

A logical to perform to perform median normalization over Nascent RNA exons rpkms, it will apply also on introns

simulatedData

A logical, set to TRUE in case the analysis is on simulated data

degDuringPulse

A logical, set to TRUE in case of a long labelling time. Also degradation of newly synthesized transcripts will be taken into account

Dmin

A numerical, it is the lower bound of the degradation rate domain for the prior optimization

Dmax

A numerical, it is the upper bound of the degradation rate domain for the prior optimization

genesFilter,

A logical which, if TRUE, filters out genes which have no signal in at least 2/3 of the time points in each feature

Value

An object of class INSPEcT with a first estimation of the rates which can be accessed by the method ratesFirstGuess.

Examples

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require(TxDb.Mmusculus.UCSC.mm9.knownGene)
txdb <- TxDb.Mmusculus.UCSC.mm9.knownGene

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

matureCounts<-allcounts$mature

testGenes<-rownames(matureCounts$exonsCounts)

require(TxDb.Mmusculus.UCSC.mm9.knownGene)
txdb<-TxDb.Mmusculus.UCSC.mm9.knownGene

exonsDB<-reduce(exonsBy(txdb ,'gene'))
exonsDB<-exonsDB[elementNROWS(range(exonsDB))==1]
intronsDB<-psetdiff(unlist(range(exonsDB)),exonsDB)
intronsDB<-intronsDB[elementNROWS(intronsDB)>0]

exWdths<-sapply(width(exonsDB),sum)
intWdths<-sapply(width(intronsDB),sum)

exWdths<-exWdths[testGenes]
intWdths<-intWdths[testGenes]
    
totalLS<-colSums(matureCounts$
  stat[c('Assigned_Exons','Assigned_Introns'),,drop=FALSE])

tpts<-c(0,1/6,1/3,1/2,1,1.5,2,4,8,12,16)
expDes<-rep(tpts,3)
    
matExp_DESeq2<-quantifyExpressionsFromTrCounts(libsize=totalLS
                                              ,exonsWidths=exWdths
                                              ,intronsWidths=intWdths
                                              ,allcounts=matureCounts
                                              ,DESeq2=TRUE
                                              ,experimentalDesign=expDes)

matureInspObj<-newINSPEcT(tpts=tpts
                         ,labeling_time=NULL
                         ,nascentExpressions=NULL
                         ,matureExpressions=matExp_DESeq2)

ste-depo/INSPEcT documentation built on July 30, 2018, 12:04 p.m.