getCistromes: getCistromes

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

getCistromes

Description

Get cistromes formed based on motif enrichment with RcisTarget

Usage

getCistromes(
  object,
  annotation = "Both",
  gene.cistrome = FALSE,
  region.cistrome = TRUE,
  nCores = 1,
  ...
)

Arguments

object	Initialized cisTopic object, after [e-mail] and [e-mail]$CtxLabels have been filled.
annotation	Annotations to be used ('TF_highConf', 'Both'). By default, only the both high confidence and indirect annotation is used.
gene.cistrome	Whether the cistromes with gene linked gene symbols have to be formed (based on the closest gene). It requires to run first annotateRegions().
region.cistrome	Whether the cistromes with regions in the data set linked to the ctx regions have to be formed (based on maximum overlap). It requires to run first scoredRegionstoCtx().
nCores	Number of cores to be used (by default 1).
...	Ignored

Value

Cistromes are stored as ctx regions ([e-mail]), regions ([e-mail]) and if specified, as gene symbols ([e-mail]). Cistromes containing extended in their name are formed by both the high confidence and indirect annotation; otherwise, only by the high confidence features.

Examples

cisTopicObject <- getCistromes(cisTopicObject, annotation = 'Both', gene.cistrome=FALSE, nCores=1)
cisTopicObject

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