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

In CSSP: ChIP-Seq Statistical Power

Description

Compute the number of reads overlapping the specified positions for a single chromosome.

Usage

bindcount.chr(tagdat, bindpos, fragL = 200, whs = 250)

Arguments

tagdat	A numeric vector of the genome coordinates for the starting positions of the aligned reads, with positive numbers representing the 5' strand and negative numbers representing the 3' strand.
bindpos	A numeric vector of the genome coordinates whose numbers of covering tags are computed.
fragL	A numeric value for the fragment length of the sequencing 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 numeric vector of the numbers of reads overlapping each position corresponding to "bindpos".

Author(s)

Chandler Zuo [e-mail]

Examples

data( tagdat_chip )
data( bindpos )
bindcount.chr( tagdat_chip[[1]], bindpos[[1]], fragL = 100, whs = 300 )

CSSP documentation built on Nov. 8, 2020, 8:26 p.m.