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

Description Usage Arguments Value Author(s) Examples

Description

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

Usage

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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 zuo@stat.wisc.edu

Examples

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