peakAnnoEnrichment: Peak Annotation Hypergeometric Enrichment in Marker Peaks.

In GreenleafLab/ArchR: Analyzing single-cell regulatory chromatin in R.

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.

Examples

# Get Test ArchR Project
proj <- getTestProject()

# Get Markers
seMarker <- getMarkerFeatures(
  ArchRProj = proj, 
  useMatrix = "PeakMatrix", 
  testMethod = "binomial", 
  binarize = TRUE
)

# Get Peak Annotation Enrichment
annoEnrich <- peakAnnoEnrichment(
  seMarker = seMarker, 
  ArchRProj = proj,
  cutOff = "FDR <= 0.1 & Log2FC >= 0"
)

GreenleafLab/ArchR documentation built on Feb. 21, 2025, 3:05 p.m.