getProfilesByBase

eSet

a probeAnno object for the given ExpressionSet

probeAnno

a data frame containing the annotation of the features of interest

gffAnno

how many basepairs upstream of the feature start (feature start on the crick strand is end in gffAnno) should be taken.

upstream

how many basepairs downtream of the feature start (feature end on the crick strand is start in gffAnno) should be taken.

character vector of chromosomes, from which the features should be taken.


This function associates the measured ChIP signals to annotated features and stores the profile of each feature in a list.
It is called by getProfiles, if method ''basewise'' is chosen. User should call this function.


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

getProfilesByBase function

This function associates the measured ChIP signals to annotated features and stores the profile of each feature in a list.
It is called by getProfiles, if method ''basewise'' is chosen. User should call this function.

getProfilesByBase: Get profiles of ChIP-signal over annotated features (basewise)

Description

Usage

Arguments

Value