get.site.count: Get site count
In DBChIP: Differential Binding of Transcription Factor with ChIP-seq

Description Usage Arguments Details Value See Also

Count number of reads around each binding site

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

`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.

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.

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).

DBChIP

DBChIP documentation built on Nov. 8, 2020, 8:27 p.m.