R: Custom bam reader

readBam {ORFik}

R Documentation

Custom bam reader

Description

Only for single end reads Safer version that handles the most important error done. In the future will use a faster .bam loader for big .bam files in R.

Usage

readBam(path, chrStyle = NULL)

Arguments

`path`	a character path to .bam file
`chrStyle`	a GRanges object, or a `seqlevelsStyle` (Default: NULL) to get seqlevelsStyle from. Is chromosome 1 called chr1 or 1, is mitocondrial chromosome called MT or chrM etc. Will use 1st seqlevel-style if more are present. Like: c("NCBI", "UCSC") -> pick "NCBI"

Value

a GAlignments object of bam file

Examples

bam_file <- system.file("extdata", "ribo-seq.bam", package = "ORFik")
readBam(bam_file, "UCSC")