getQTLFeatures: Get annotation of features within QTL intervals.

In gact/shmootl: QTL Analysis Utilities for Yeast

Description

Get annotation of features within QTL intervals.

Usage

getQTLFeatures(qtl.intervals, features)

Arguments

qtl.intervals	A qtlintervals object.
features	A data.frame of primary genome features, as returned by readFeaturesGFF. For each feature, this data.frame must include the reference sequence ('chr'), 1-offset base-pair positions of the start and end of the feature ('start' and 'end' respectively), and the feature 'ID'.

Details

Overlaps between intervals are identified with the function GenomicRanges::findOverlaps, which regards two intervals as overlapping if they have at least one overlapping position. Because of this, features that do not lie completely within a given QTL interval may be included in the returned qtlfeatures object. Such partial overlaps should treated with caution.

Value

An object of class qtlfeatures, which is essentially a list of data.frame objects, each containing the set of genome features in a given QTL interval.

See Also

Other QTL functions: estPhysicalPositions, getQTLIntervals, getQTLPeaks, plotQTLScanone

gact/shmootl documentation built on Nov. 11, 2021, 6:23 p.m.