countsBetweenAnchors-methods: Summarise interactions between anchors

In LTLA/fugi: Further Utilities for Genomic Interactions

Description

Calculate the number of of paired-end reads mapping between a defined set of anchors. This function will ignore counts present in the input data.

Usage

countsBetweenAnchors(x, y, ...)

## S4 method for signature 'GenomicInteractions,GRanges'
countsBetweenAnchors(x, y,
  ignore_overlaps = FALSE, ...)

Arguments

x	A GenomicInteractions object.
y	A GenomicRanges object.
...	Extra parameters to pass to findOverlaps for GenomicInteractions objects.
ignore_overlaps	Logical scalar indicating whether overlapping anchors should be disallowed.

Details

By default, ignore_overlaps=FALSE will raise an error when overlapping anchors are observed. This can be turned off but users should be careful with multi-mapping. Setting type="within" in findOverlaps can reduce multi-mapping effects.

Value

A GenomicInteractions object with annotated counts between anchors.

LTLA/fugi documentation built on June 22, 2019, 8:50 p.m.