CSSP (version 1.10.0)

peakcount: Compute the number of aligned reads overlapping the specified peak intervals for the whole genome.

Description

Compute the number of aligned reads overlapping the specified peak intervals for the whole genome.

Usage

peakcount(chipdat, inputdat, peakpos, fragL = 200, unique = FALSE)

Arguments

chipdat

A list of the starting positions of the ChIP sample aligned reads for each chromosome. The sign of each coordinate represents its strand direction, with a positive numbers on the 5' strand and a negative numbers on the 3' strand.

inputdat

A list of the starting positions of the input sample aligned reads for each chromosome. The sign of each coordinate represents its strand direction, with a positive numbers on the 5' strand and a negative numbers on the 3' strand.

peakpos

A list containing the genome coordinates for each peak interval on each chromosome. Each list component is a 2-column matrix containing the left and right boundary of the peak intervals on one chromosome.

fragL

A numeric value of the fragment length of the aligned reads. Default: 200.

unique

A logical value for whether only reads mapping to unique nucleotide positions are counted.

Value

A list of the numbers of reads that overlap the corresponding peak intervals.

Examples

data( peakpos )
data( tagdat_input )
data( tagdat_chip )
peakcount( tagdat_chip, tagdat_input, peakpos, fragL = 100 )