topicSignaturesMatrix: topicSignaturesMatrix

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

topicSignaturesMatrix

Description

Matrix containing the row normalised AUC values for the signatures in the topics.

Usage

topicSignaturesMatrix(
  object,
  topics = "all",
  selected.signatures = "all",
  nCores = 4,
  aucMaxRank = 0.03 * nrow(aucellRankings),
  scale = TRUE,
  ...
)

Arguments

object	Initialized cisTopic object, after regions scores have been calculated with getRegionScores and object@signatures is filled.
topics	By default all topics will be used, but topics can be selected based on index.
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
scale	Whether AUC enrichment should be normalized
...	See Heatmap from ComplexHeatmap

Value

Matrix containing the enrichment per topic per signature

Examples

###
# Load cisTopic object:
path2cisTopicObject <- system.file(package="cisTopic", "examples/cisTopicObject_melanoma.Rds")
cisTopicObject <- readRDS(path2cisTopicObject)
###

signatureMatrix <- topicSignaturesMatrix(cisTopicObject)

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