get.site.count {DBChIP} | R Documentation |
Count number of reads around each binding site
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 |
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). |