ma.stat

regID

start

stop

logR

frag.length

estimated center of the unbound probes from <code><a rd-options="" href="/link/backgd.sd?package=Starr&version=1.28.0" data-mini-rdoc="Starr::backgd.sd">backgd.sd</a></code>.

center

estimated standard deviation of the unbound probes <code><a rd-options="" href="/link/backgd.sd?package=Starr&version=1.28.0" data-mini-rdoc="Starr::backgd.sd">backgd.sd</a></code>.

sigma

autocorrelation functions for maximum window size/lag of 30 probes <code><a rd-options="" href="/link/backgd.sd?package=Starr&version=1.28.0" data-mini-rdoc="Starr::backgd.sd">backgd.sd</a></code>.

option for sliding window, either "fixed.probe" or "fixed.gen.dist". Default is 'fixed.probe'.

window.opt


  An internal function to be used by  <code><a rd-options="" href="/link/cmarrt.ma?package=Starr&version=1.28.0" data-mini-rdoc="Starr::cmarrt.ma">cmarrt.ma</a></code>.


internal

Starr facilitates the analysis of ChIP-chip data, in particular that of Affymetrix tiling arrays. The package provides functions for data import, quality assessment, data visualization and exploration. Furthermore, it includes high-level analysis features like association of ChIP signals with annotated features, correlation analysis of ChIP signals and other genomic data (e.g. gene expression), peak-finding with the CMARRT algorithm and comparative display of multiple clusters of ChIP-profiles. It uses the basic Bioconductor classes ExpressionSet and probeAnno for maximum compatibility with other software on Bioconductor. All functions from Starr can be used to investigate preprocessed data from the Ringo package, and vice versa. An important novel tool is the the automated generation of correct, up-to-date microarray probe annotation (bpmap) files, which relies on an efficient mapping of short sequences (e.g. the probe sequences on a microarray) to an arbitrary genome.

Benedikt Zacher

Starr

Simple tiling array analysis of Affymetrix ChIP-chip data

ma.stat function

estimated center of the unbound probes from <code><a href="backgd.sd" rd-options="">backgd.sd</a></code>.

estimated standard deviation of the unbound probes <code><a href="backgd.sd" rd-options="">backgd.sd</a></code>.

autocorrelation functions for maximum window size/lag of 30 probes <code><a href="backgd.sd" rd-options="">backgd.sd</a></code>.

An internal function to be used by  <code><a href="cmarrt.ma" rd-options="">cmarrt.ma</a></code>.

Compute moving average statistics and p-values

unstandardized moving average(MA) statistics.

standardized MA under correlation structure.

z.cmarrt

standardized MA under independence (ignoring correlation structure).

z.indep

pv.cmarrt

p-values of probes under independence (ignoring correlation structure).

ma.stat: Compute moving average statistics and p-values

Description

Usage

Arguments

Value

References

See Also