getFeature

feature

mapping

expr_mat

a data frame, containing the gff annotation

gffAnno

character or integer, indicating the chromosome

if true, profiles on the crick strand are reversed, so they are in the right order

reverse


This function gets the probe intensities of a feature, that was mapped, using the mapFeatures function. 
It is called by the getIntensities function method, if method "middle" is chosen in getProfiles.


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

getFeature function

This function gets the probe intensities of a feature, that was mapped, using the mapFeatures function. 
It is called by the getIntensities function method, if method "middle" is chosen in getProfiles.

getFeature: Getting profiles of one annotated features with a given mapping

Description

Usage

Arguments

Value