DBChIP (version 1.16.0)

get.site.count: Get site count

Description

Count number of reads around each binding site

Usage

get.site.count(dat, subtract.input=FALSE, window.size = 250)

Arguments

dat

a list with the following items: consensus.site, chip.list, input.list, matching.input.names, norm.factor.vec. Description of the items can be found in the return value of DBChIP.

subtract.input

logical. Whether input will be subtracted from ChIP when counting the binding reads. Default is FALSE.

window.size

the window size to count reads around each binding site. Default 250 bp.

Value

This function return the incoming dat with the new component:

site.count

a matrix of read counts for each site (row) and each ChIP library (column).

Details

The read count for each binding site is defined as the sum of the number of 5' ends on the positive strand within the upstream window [s-w, s-1] and the number of 5' ends on the negative strand within the downstream window [s+1, s+w], where s is a consensus site position and w is the window size parameter.

See Also

DBChIP