bpmapToProbeAnno

 	Either a list, created by the function readBpmap() from the affy package. Or a path to the bpmap file. 

 bpmap

verbose

 If TRUE, probes sequences that occur more than once on the chip (and consequently match several positions on the genome) are set to 1 in the probeAnno object. Unique probes are set to 0. If false, all probes are set to 0. To identify all unique and multiple matching probes, a remapping of the probes to the genome is recommended.

uniqueSeq

This function allows the user to create a probeAnno environment that holds the mapping between
probes on the array and their genomic match position(s). The function takes an Affymetrix bpmap file as input.

manip

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

bpmapToProbeAnno function

Either a list, created by the function readBpmap() from the affy package. Or a path to the bpmap file.

bpmap

If TRUE, probes sequences that occur more than once on the chip (and consequently match several positions on the genome) are set to 1 in the probeAnno object. Unique probes are set to 0. If false, all probes are set to 0. To identify all unique and multiple matching probes, a remapping of the probes to the genome is recommended.

This function allows the user to create a probeAnno environment that holds the mapping between
probes on the array and their genomic match position(s). The function takes an Affymetrix bpmap file as input.

bpmapToProbeAnno: Creating a probeAnno object

Description

Usage

Arguments

Examples