|
6
|
1 \name{add.broad.peak.regions}
|
|
|
2 \alias{add.broad.peak.regions}
|
|
|
3 %- Also NEED an '\alias' for EACH other topic documented here.
|
|
|
4 \title{ Calculate chromosome-wide profiles of smoothed tag density }
|
|
|
5 \description{
|
|
|
6 Looks for broader regions of enrichment associated with the determined
|
|
|
7 peak positions, adds them to the $npl data as $rs, $re columns.
|
|
|
8 }
|
|
|
9 \usage{
|
|
|
10 add.broad.peak.regions(signal.tags, control.tags, binding.postions,window.size=500,z.thr=2)
|
|
|
11 }
|
|
|
12 %- maybe also 'usage' for other objects documented here.
|
|
|
13 \arguments{
|
|
|
14 \item{signal.tags}{ signal chromosome tag coordinate vectors (e.g. output
|
|
|
15 of \code{\link{select.informative.tags}} }
|
|
|
16 \item{control.tags}{ optionall control (input) tags }
|
|
|
17 \item{binding.positions}{ output of find.binding.positions call }
|
|
|
18 \item{window.size}{ window size to be used in calculating enrichment }
|
|
|
19 \item{z.thr}{ Z-score corresponding to the Poisson ratio threshold
|
|
|
20 used to flag significantly enriched windows}
|
|
|
21 }
|
|
|
22 \value{
|
|
|
23 A structure identical to binding.postions with two additional columns
|
|
|
24 added (rs and re) corresponding to start and end of the associated
|
|
|
25 significantly enriched region. If no region was associated with a
|
|
|
26 particular peak, NAs values are reported.
|
|
|
27 }
|
