View source: R/OverlapcisTopic.R
signatureCellEnrichment | R Documentation |
Determine signatures enrichment in the cells. If specified, signature enrichment can be plotted.
signatureCellEnrichment(
object,
aucellRankings,
selected.signatures = "all",
nCores = 1,
aucMaxRank = 0.03 * nrow(aucellRankings),
plot = TRUE,
...
)
object |
Initialized cisTopic object, after object@cistromes.regions have been filled (see |
aucellRankings |
Precomputed aucellRankings using |
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 |
AUC enrichment values for the signature are stored as a column in object@cell.data. If specified, cells coloured by their AUC enrichment values will be plotted.
pred.matrix <- predictiveDistribution(cisTopicObject)
aucellRankings <- AUCell_buildRankings(pred.matrix)
cisTopicObject <- signatureCellEnrichment(cisTopicObject, aucellRankings, nCores=1)
cisTopicObject
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