sameLength

distribution

character vector, indicating which regions of profiles should be made the same length. Only upstream and downstream are available.

method


This function makes equal length of upstream and downstream regions in a profile list.
It is called by getProfiles if method ''middle'' is chosen and sameLength=T.


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

sameLength function

This function makes equal length of upstream and downstream regions in a profile list.
It is called by getProfiles if method ''middle'' is chosen and sameLength=T.

sameLength: Make equal length of upstream and downstream regions in a profile list

Description

Usage

Arguments