declare.bound

error rate control for declaring bound region.

alpha

correction method inherited from <code><a rd-options="" href="/link/p.adjust?package=Starr&version=1.28.0" data-mini-rdoc="Starr::p.adjust">p.adjust</a></code>.

method

a numeric vector of p-values for MA statistics obtained under correlation structure via Gaussian approximation.

pv.cmarrt

a numeric vector of p-values for MA statistics obtained under independence via Gaussian approximation.

pv.indep


  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

declare.bound function

correction method inherited from <code><a href="p.adjust" rd-options="">p.adjust</a></code>.

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

declare.bound: Declare bound probes for a given error rate control

Description

Usage

Arguments

Value

References

See Also