bindcount: Compute the number of reads overlapping the specified...

In chandlerzuo/cssp: ChIP-Seq Statistical Power

Description

Compute the number of reads overlapping the specified positions for the whole genome.

Usage

bindcount(chipdat, inputdat, bindpos, fragL = 200, whs = 250)

Arguments

chipdat	A list of the starting coordinates for aligned reads for all chromosomes, with positive numbers representing the 5' strand and negative numbers representing the 3' strand.
inputdat	A list of the starting coordinates for aligned reads for the input sample for all chromosomes, with positive numbers representing the 5' strand and negative numbers representing the 3' strand.
bindpos	A list of genome coordinates for each chromosome whose numbers of covering tags are computed.
fragL	A numeric value for the fragment length of the aligned reads. Default: 200.
whs	A numeric value for the half window size around the binding position. All tags overlapping this region are counted. Default: 250.

Value

A list of the number of overlapping tags for all position. Each list is a data.frame corresponding to a single chromosome, containing:

chip	The number of ChIP sample reads overlapping each position.
input	The number of input sample reads overlapping each position.

Author(s)

Chandler Zuo [e-mail]

Examples

data( tagdat_input )
data( tagdat_chip )
data( bindpos )
bindcount( tagdat_chip, tagdat_input, bindpos, fragL = 100, whs = 300 )

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