yCrypticRNAs (version 0.99.2)

bam_to_reads: Convert BAM files into BED files containing the reads overlaping the specified annotations.

Description

Convert BAM files into BED files containing the reads overlaping the specified annotations.

Usage

bam_to_reads(bamfile, annotations, paired_end = TRUE, as_fragments = TRUE, outfile = NULL, flanking_region = 0)

Arguments

bamfile

a character vector indicating the BAM file name. Note: The bamfile must be sorted by coordinates.

annotations

an object of type annotationsSet containing information on one genes.

paired_end

logical indicating whether the bamfile contains paired-end data.

as_fragments

logical indicating if paired-end data must be paired and merged to form fragments.

outfile

a character vector indicating the output file name. If not provided, the result will be internalized in R.

flanking_region

Number of bases before and after the gene ORF should be included.

Value

An object of type data.table with 9 columns.

chromosome

Read chromosome.

start

Read starting position.

end

Read ending position.

name

Query template name .

score

Mapping quality.

ChromosomeNext

Gene strand.

startNext

Position of the mate/next read.

tlen

observed read length.

Examples

bamfile <- system.file("extdata", "wt_rep1.bam", package = "yCrypticRNAs")
data(annotations)
bam_to_reads(bamfile, annotations)