GetPileUpPerGene: Get read depths per gene as defined by the RSamtools pileup...

In njmadrid/RNAseqQuality: Provides a set of functions for summarizing the quality of RNA-seq data.

Description

Get read depths per gene as defined by the RSamtools pileup function.

Usage

GetPileUpPerGene(BamFilePath, TopCDSDF, max_depth = 10000)

Arguments

BamFilePath	Location of aligned bam file. Corresponding bai index file must be in the same directory.
TopCDSDF	Data frame of CDS returned from select(Homo.sapiens).
max_depth	Parameter of the same name passed to Rsamtools pileup. Default value is 10000.

Value

A data.frame created via Rsamtools:pileup for each CDS region in TopCDSDF.

Author(s)

Nathaniel J. Madrid, Jason Byars

Examples

BamFilePaths <- dir(path="/home/ubuntu/BamFiles", pattern=".*.bam$", full.names=T)
TopGenesDF <- data.frame(gene = c("NM_016824", "NM_019903", "NP_001112"))
cdsColumns <- c("CDSCHROM", "CDSSTART", "CDSEND", "CDSSTRAND", "SYMBOL")
TopCDSDF <- select(Homo.sapiens, keys=as.character(TopGenesDF$gene), columns=cdsColumns, keytype="REFSEQ")
TopCDSDF$CDSCHROM <- sub("chr", "", TopCDSDF$CDSCHROM)
TopCDSDF <- TopCDSDF[which(TopCDSDF$CDSCHROM %in% c(1:22, "X", "Y")), ]
PileUpPerFile <- lapply(BamFilePaths[1:3], function(f) GetPileUpPerGene(f, TopCDSDF)) 

njmadrid/RNAseqQuality documentation built on May 20, 2019, 3:32 p.m.