diff spp/man/get.broad.enrichment.clusters.Rd @ 15:e689b83b0257 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spp/man/get.broad.enrichment.clusters.Rd	Tue Nov 27 16:15:21 2012 -0500
@@ -0,0 +1,27 @@
+\name{get.broad.enrichment.clusters}
+\alias{get.broad.enrichment.clusters}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{ Determine broad clusters of enrichment }
+\description{
+  Scan chromosomes with a pre-defined window size, comparing scaled ChIP
+  and input tag coutns to see if their ratio exceeds that expected from
+  a Poisson process (normalized for dataset size).
+}
+\usage{
+get.broad.enrichment.clusters(chip.tags, input.tags, window.size=1e3,z.thr=3,tag.shift=146/2)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{chip.tags}{ foreground tag vector list }
+  \item{input.tags}{ background tag vector list }
+  \item{window.size}{ window size to be used for tag counting }
+  \item{z.thr}{ Z-score to be used as a significance threshold }
+  \item{tag.shift}{ number of base pairs by which positive and negative
+    tag coordinates should be shifted towards eachother (half of binding
+  peak separation distance)}
+}
+\value{
+  A list of elements corresponding to chromosomes, with each element
+  being an $s/$e/$rv data.frame giving the starting, ending positions and the log2
+  enrichment estimate for that region.
+}