peakcount.chr: Compute the number of aligned reads overlapping peaks for one...

In chandlerzuo/cssp: ChIP-Seq Statistical Power

Description

Compute the number of aligned reads overlapping peaks for one chromosome.

Usage

peakcount.chr(tagdat, peakpos, fragL = 200, unique = FALSE)

Arguments

tagdat	A numeric vector of the genome coordinates for the starting positions of aligned reads. The signs of coordinates represent their strand direction, with positive numbers representing the 5' strand and negative numbers representing the 3' strand.
peakpos	A 2-column matrix matrix containing the left and right position of the peaks for one chromosome.
fragL	A numeric value for the fragment length of the sequencing reads. Default: 200.
unique	A logical value for whether only reads mapping to unique nucleotide positions are counted.

Value

A numeric vector of the number of overlapping tags for all peaks.

Author(s)

Chandler Zuo [e-mail]

Examples

data( peakpos )
data( tagdat_input )
peakcount.chr( tagdat_input[[1]], peakpos[[1]], fragL = 100 )

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