mapFeatures: Map middle positions of probes to annotated features

Description Usage Arguments Value Author(s)

View source: R/getProfilesMiddle.R

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

1
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 zacher@lmb.uni-muenchen.de


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