binarizedcisTopicsToCtx: binarizedcisTopicsToCtx

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

binarizedcisTopicsToCtx

Description

Convert binarized cisTopics to the corresponding cisTarget coordinates

Usage

binarizedcisTopicsToCtx(object, genome, liftOver = NULL, minOverlap = 0.4, ...)

Arguments

object	Initialized cisTopic object, after the [e-mail] has been filled.
genome	Genome to which the data has been mapped. If you are using liftOver, provide the genome to which you data has been lift-overed. The available genomes are hg19, dm3, dm6 and mm9.
liftOver	GRangesList object containing the original coordinates (in the same format as [e-mail]) in the data set as slot names and the corresponding mapping regions as a GRanges object in the slot.
...	See findOverlap from GenomicRanges

Value

Returns the cisTarget regions that correspond to the binarized topics in [e-mail]

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