bam_to_reads: Convert BAM files into BED files containing the reads...

In yCrypticRNAs: Cryptic Transcription Analysis in Yeast

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.
flag	bitwise flag.

Examples

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

yCrypticRNAs documentation built on May 29, 2017, 5:49 p.m.