quantifyExpressionsFromBAMs: Evaluate introns and exons expressions from BAM or SAM files

Description Usage Arguments Value Examples

View source: R/quantifyExpressionsFromBAMs.R

Description

Given a TranscriptDb object and a list of BAM or SAM files "quantifyExpressionsFormBAMs" evaluates exons and introns expressions and the associated variances per each gene.

Usage

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quantifyExpressionsFromBAMs(txdb, BAMfiles, experimentalDesign, by = c("gene",
  "tx"), countMultiMappingReads = FALSE, allowMultiOverlap = FALSE,
  strandSpecific = 0, isPairedEnd = FALSE, DESeq2 = TRUE,
  varSamplingCondition = NULL)

Arguments

txdb

A TranscriptDB object

BAMfiles

A vector of paths

experimentalDesign

A numerical which reports the desing of the experiment in terms of time points and replicates. Time points must be ordered according to the sequence of files submitted for the analysis, these labels characterize different files as replicates of a given condition.

by

A character, either "gene" or "tx", indicating if expressions and counts should be summarized at the levels of genes or transcripts. "gene" by default

countMultiMappingReads

A logical, if multimapping reads should be counted, FALSE by default. Multimap reads are identified using the tag "NH" in the bam/sam file.

allowMultiOverlap

A logical, indicating if a read is allowed to be assigned to more than one feature, FALSE by default

strandSpecific

Numeric, 0 if no strand-specific read counting should be performed, 1 stranded, 2 reversely-stranded. 0 by default

isPairedEnd

A logical, if paired-end reads are used, FALSE by default

DESeq2

A logical, if TRUE exons and introns variances are evaluated through the package DESeq2, if FALSE through plgem

varSamplingCondition

A character reporting which experimental condition should be used to sample the variance if DESeq2 = FALSE

Value

A list containing expressions and associated variances for exons and introns.

Examples

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require(TxDb.Mmusculus.UCSC.mm9.knownGene)
txdb<-TxDb.Mmusculus.UCSC.mm9.knownGene
expDes<-c(0,0,1,1)

paths_total<-system.file('extdata/', c('bamRep1.bam'
                                      ,'bamRep2.bam'
                                      ,'bamRep3.bam'
                                      ,'bamRep4.bam')
                        ,package='INSPEcT')
matExp<-quantifyExpressionsFromBAMs(txdb=txdb
                                   ,BAMfiles=paths_total
                                   ,DESeq2=TRUE
                                   ,experimentalDesign=expDes)

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