mapFeatures: Map middle positions of probes to annotated features

In Starr: Simple tiling array analysis of Affymetrix ChIP-chip data

Description

This function maps the middle positions of probes to annotated features. It is called by the getProfiles method, if method "middle" is chosen.

Usage

mapFeatures(probeAnno, gffAnno, upstream, downstream, chr)

Arguments

probeAnno	a probeAnno object for the given ExpressionSet
gffAnno	a data frame containing the annotation of the features of interest
upstream	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.
chr	character vector of chromosomes, from which the features should be taken.

Value

a list with one entry for each feature, containing the mapping to probe indices in the assayData.

Author(s)

Benedikt Zacher [e-mail]

Starr documentation built on April 28, 2020, 7:52 p.m.