fOverlaps: Find overlaps

In svenbioinf/OGRE: Calculate, visualize and analyse overlap between genomic regions

Find overlaps

Description

Finds all overlaps between query and subject(s) and stores each hit (overlap) in data table detailDT. Data table sumDT shows all overlaps of a certain subject type for all query elements. By default also partially overlaps are reported. Overlap calculation is done using GenomicRanges::findOverlaps() implementation.

Usage

fOverlaps(OGREDataSet, selfHits = FALSE, ignoreStrand = TRUE, ...)

Arguments

OGREDataSet	A OGREDataSet.
selfHits	logical if FALSE(default) ignores self hits of identical regions (with identical IDs) within datasets.
ignoreStrand	logical If TRUE (default) two regions with overlapping locations on different strands are considered an overlap hit.
...	Additional parameters, see GenomicRanges::findOverlaps()

Value

OGREDataSet.

Examples

myOGRE <- makeExampleOGREDataSet()
myOGRE <- loadAnnotations(myOGRE)
myOGRE <- fOverlaps(myOGRE)

svenbioinf/OGRE documentation built on Jan. 30, 2023, 10:55 p.m.