rm.small.peak

vector of 0's(unbound) or 1's(bound) for each probe. 

bdd.method

minimum number of probes to be called a bound region.

minrun

start

stop


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

rm.small.peak function

vector of 0's(unbound) or 1's(bound) for each probe.

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

Remove bound regions which consist of too few probes

number of probes within each bound region.

size:

first probe location for each bound region.

peak.start

last probe location for each bound region.

rm.small.peak: Remove bound regions which consist of too few probes

Description

Usage

Arguments

Value

Details

References

See Also