diff spp/man/add.broad.peak.regions.Rd @ 6:ce08b0efa3fd draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spp/man/add.broad.peak.regions.Rd	Tue Nov 27 16:11:40 2012 -0500
@@ -0,0 +1,27 @@
+\name{add.broad.peak.regions}
+\alias{add.broad.peak.regions}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{ Calculate chromosome-wide profiles of smoothed tag density }
+\description{
+  Looks for broader regions of enrichment associated with the determined
+  peak positions, adds them to the $npl data as $rs, $re columns. 
+}
+\usage{
+add.broad.peak.regions(signal.tags, control.tags, binding.postions,window.size=500,z.thr=2)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{signal.tags}{ signal chromosome tag coordinate vectors (e.g. output
+    of \code{\link{select.informative.tags}} }
+  \item{control.tags}{ optionall control (input) tags }
+  \item{binding.positions}{ output of find.binding.positions call }
+  \item{window.size}{ window size to be used in calculating enrichment }
+  \item{z.thr}{ Z-score corresponding to the Poisson ratio threshold
+    used to flag significantly enriched windows}
+}
+\value{
+  A structure identical to binding.postions with two additional columns
+  added (rs and re) corresponding to start and end of the associated
+  significantly enriched region. If no region was associated with a
+  particular peak, NAs values are reported.
+}