diff spp/man/get.binding.characteristics.Rd @ 15:e689b83b0257 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spp/man/get.binding.characteristics.Rd	Tue Nov 27 16:15:21 2012 -0500
@@ -0,0 +1,55 @@
+\name{get.binding.characteristics}
+\alias{get.binding.characteristics}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{ Calculate characteristics of observed DNA-binding signal from
+  cross-correlation profiles }
+\description{
+  The methods calculates strand cross-correlation profile to determine binding
+  peak separation distance and approximate window size that should be used
+  for binding detection. If quality scores were given for the tags,
+  which quality bins improve the cross-correlation pattern.
+}
+\usage{
+get.binding.characteristics(data, srange = c(50, 500), bin = 5, cluster = NULL, debug = F, min.tag.count = 1000, acceptance.z.score = 3, remove.tag.anomalies = T, anomalies.z = 5,accept.all.tags=F)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{data}{ Tag/quality data: output of \code{read.eland.tags} or similar function }
+  \item{srange}{ A range within which the binding peak separation is
+    expected to fall. Should be larger than probe size to avoid artifacts. }
+  \item{bin}{ Resolution (in basepairs) at which cross-corrrelation
+    should be calculated. bin=1 is ideal, but takes longer to calculate. }
+  \item{cluster}{ optional snow cluster for parallel processing }
+  \item{debug}{ whether to print debug messages }
+  \item{min.tag.count}{ minimal number of tags on the chromosome to be
+    considered in the cross-correlation calculations }
+  \item{acceptance.z.score}{ A Z-score used to determine if a given tag
+    quality bin provides significant improvement to the strand cross-correlation }
+  \item{remove.tag.anomalies}{ Whether to remove singular tag count peaks prior to
+  calculation. This is recommended, since such positions may distort the
+  cross-correlation profile and increase the necessary computational time. }
+  \item{anomalies.z}{ Z-score for determining if the number of tags at a
+  given position is significantly higher about background, and should be
+  considered an anomaly.}
+  \item{accept.all.tags}{ Whether tag alignment quality calculations
+    should be skipped and all available tags should be accepted in the
+    downstream analysis.}
+}
+\value{
+  \item{cross.correlation }{ Cross-correlation profile as an $x/$y data.frame}
+  \item{peak }{Position ($x) and height ($y) of automatically detected
+    cross-correlation peak.}
+  \item{whs} { Optimized window half-size for binding detection (based
+    on the width of the cross-correlation peak) }
+  \item{quality.bin.acceptance} { A list structure, describing the
+    effect of inclusion of different tag quality bins on
+    cross-correlation, and a resolution on which bins should be
+    considered.
+    \item{informative.bins} { A boolean vector indicating whether the
+      inclusion of tags from the tag quality bin specified in the name
+      attribute significantly increases cross-correlation profile near
+      the peak.}
+    \item{quality.cc} { A list giving the cross-correlation profile
+      after the inclusion of the tags from different quality bins }
+    }
+}