peakcount: Compute the number of aligned reads overlapping the specified...

In chandlerzuo/cssp: ChIP-Seq Statistical Power

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.

Author(s)

Chandler Zuo [e-mail]

Examples

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

chandlerzuo/cssp documentation built on May 13, 2019, 3:23 p.m.