INSPEcT (version 1.2.2)

makeRPKMs: Calculate RPKM and count values on introns and exons from bam/sam files

Description

Given a TranscriptDb object and a list of bam/sam files for 4su and total RNA experiments, "makeRPKMs" function calculates read counts and RPKM on exonic and intronic features per each gene. Reads that fall where intronic and exonic features overlaps are univoquely assigned to exons.

Usage

makeRPKMs(txdb, paths_foursu, paths_total, by = c("gene", "tx"), countMultiMappingReads = FALSE, allowMultiOverlap = FALSE, strandSpecific = FALSE, isPairedEnd = FALSE)

Arguments

txdb

A TranscriptDB object

paths_foursu

A vector of paths of 4sU-seq sam files

paths_total

A vector of paths of RNA-seq sam files

by

A character, either "gene" or "tx", indicating if rpkms 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

A logical, if strand-specific read counting should be performed, FALSE by default

isPairedEnd

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

Value

A list containing rpkms, counts and the annotation extracted from TxDB for exons and introns

Examples

require(TxDb.Mmusculus.UCSC.mm9.knownGene)
txdb <- TxDb.Mmusculus.UCSC.mm9.knownGene
files4su <- system.file('extdata', '4sURNA_0h.bam', package="INSPEcT")
filesTotal <- system.file('extdata', 'totalRNA_0h.bam', package="INSPEcT")
makeRPKMsOut <- makeRPKMs(txdb, files4su, filesTotal)
rpkms <- makeRPKMsOut$rpkms
counts <- makeRPKMsOut$counts
annotation <- makeRPKMsOut$annotation