seqbias (version 1.20.0)

count.reads: Counting reads across intervals

Description

Counts the number of reads starting at each position across given genomic intervals

Usage

count.reads(reads_fn, I, sb=NULL, binary=FALSE, sum.counts=FALSE)

Arguments

reads_fn

filename of aligned reads in BAM format

I

a GRanges object giving valid genomic intervals

sb

a seqbias object

binary

if TRUE, return a 0-1 vector, otherwise return a vector counting the number of reads mapped to each position

sum.counts

if TRUE return the total read count for each interval

Value

A list of numeric vectors is returned, one for each interval provided. Each vector gives an integer count of the number of reads beginning on that position.

Details

Given an indexed BAM file, this function counts the number of reads starting at each position of each provided interval. If a seqbias object is provided through the sb attribute, counts are corrected for sequence bias. The total read count for each interval is returned if sum.counts is TRUE. If binary is TRUE a 0-1 vector is returned instead, where positions at which no reads are mapped are 0, and those with one or more are 1.

See Also

seqbias.predict

Examples

  reads_fn <- system.file( "extra/example.bam", package = "seqbias" )

  I <- GRanges( c('seq1'), IRanges( c(1), c(5000) ), strand = c('-') )

  counts <- count.reads( reads_fn, I )