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

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.

Examples

Run this code

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

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