getCistromeEnrichment: getCistromeEnrichment

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

getCistromeEnrichment

Description

Determine topic-specific cistrome enrichment in the cells. If specified, cistrome enrichment can be plotted.

Usage

getCistromeEnrichment(
  object,
  topic,
  TFname,
  annotation = "TF_highConf",
  aucellRankings,
  nCores = 1,
  aucMaxRank = 0.03 * nrow(aucellRankings),
  plot = TRUE,
  ...
)

Arguments

object	Initialized cisTopic object, after [e-mail] have been filled (see getCistromes()).
topic	Topic number of the cistrome.
TFname	Name of the transcription factor linked to the cistrome.
annotation	Annotations to be used ('TF_highConf', 'Both'). By default, only the high confidence annotation is used.
aucellRankings	Precomputed aucellRankings using cisTopic_buildRankings(). These rankings are not stored in the cisTopicObject due to their size.
nCores	Number of cores to be used for AUCell
aucMaxRank	Threshold to calculate the AUC
plot	Whether enrichment plot should be done. If yes, parameters for plotFeatures will not be ignored.
...	See plotFeatures().

Value

AUC enrichment values for the signature are stored as a column in [e-mail]. If specified, cells coloured by their AUC enrichment values will be plotted.

Examples

cisTopicObject <- getCistromeEnrichment(cisTopicObject, annotation = 'Both', nCores=1)
cisTopicObject

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