signatureCellEnrichment: signatureCellEnrichment

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

signatureCellEnrichment

Description

Determine signatures enrichment in the cells. If specified, signature enrichment can be plotted.

Usage

signatureCellEnrichment(
  object,
  aucellRankings,
  selected.signatures = "all",
  nCores = 1,
  aucMaxRank = 0.03 * nrow(aucellRankings),
  plot = TRUE,
  ...
)

Arguments

object	Initialized cisTopic object, after [e-mail] have been filled (see getCistromes()).
aucellRankings	Precomputed aucellRankings using AUCell_buildRankings(). These rankings are not stored in the cisTopicObject due to their size.
selected.signatures	By default all signatures will be used, but signatures can be selected based on index or name. Alternatively, 'annotation' can be selected to use as signatures the region type labels (e.g. promoter, distal intergenic, ...) For this, the function annotateRegions() must be run first.
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

pred.matrix <- predictiveDistribution(cisTopicObject)
aucellRankings <- AUCell_buildRankings(pred.matrix)
cisTopicObject <-  signatureCellEnrichment(cisTopicObject, aucellRankings, nCores=1)
cisTopicObject

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