getSignaturesRegions: getSignaturesRegions

In aertslab/cisTopic: cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data

getSignaturesRegions

Description

Get peaks found in region signatures given as a bed files and/or dataframes

Usage

getSignaturesRegions(object, signatures, labels, minOverlap = 0.4, ...)

Arguments

object	Initialized cisTopic object.
labels	A character vector with the names to be given to the signatures (in the same order as the signature paths or named)
minOverlap	Minimum overlap between the regions to consider them as overlapping regions
...	See findOverlaps from GenomicRanges
signature	Path to bed file or data frame containing signature regions (or a vector)

Value

The regions from the dataset that overlap with the signature are returned as a slot to object@signatures

Examples

regions <- c('regions_1.bed', 'regions_2.bed', 'regions_3.bed')
cisTopicObject <- getSignaturesRegions(cisTopicObject, regions)
cisTopicObject

aertslab/cisTopic documentation built on April 6, 2024, 9:31 p.m.