match_ac

Set of sequences, given as a character vector

 dictionary

At least one text, to match the sequences to.

text

If TRUE, the sequences are searched in the complementary strand of the text

complementary

If TRUE, the sequences are searched in the reverse strand of the text

reverse

If TRUE, the sequences are searched in the reverse complementary strand of the text

reverse_complementary

nseq


The Algorithm is designed to match a given set of sequences to a text. This function is used by remap for mapping reporter sequences to the genome.


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

match_ac function

dictionary

The Algorithm is designed to match a given set of sequences to a text. This function is used by remap for mapping reporter sequences to the genome.

match_ac: Exact String matching using the Aho-Corasick algorithm

Description

Usage

Arguments