peakAnnoEnrichment: Peak Annotation Hypergeometric Enrichment in Marker Peaks.
In haibol2016/ArchR_debug: Analyzing single-cell regulatory chromatin in R.

peakAnnoEnrichment

R Documentation

Peak Annotation Hypergeometric Enrichment in Marker Peaks.

Description

This function will perform hypergeometric enrichment of a given peak annotation within the defined marker peaks.

Usage

peakAnnoEnrichment(
  seMarker = NULL,
  ArchRProj = NULL,
  peakAnnotation = NULL,
  matches = NULL,
  cutOff = "FDR <= 0.1 & Log2FC >= 0.5",
  background = "all",
  logFile = createLogFile("peakAnnoEnrichment")
)

Arguments

`seMarker`	A `SummarizedExperiment` object returned by `markerFeatures()`.
`ArchRProj`	An `ArchRProject` object.
`peakAnnotation`	A `peakAnnotation` object in the provided `ArchRProject` to be used for hypergeometric testing.
`matches`	A custom `peakAnnotation` matches object used as input for the hypergeometric test. See `motifmatchr::matchmotifs()` for additional information.
`cutOff`	A valid-syntax logical statement that defines which marker features from `seMarker` to use. `cutoff` can contain any of the `assayNames` from `seMarker`.
`background`	A string that indicates whether to use a background set of matched peaks to compare against ("bgdPeaks") or all peaks ("all").
`logFile`	The path to a file to be used for logging ArchR output.