This function will add total counts of scATAC cells in provided features into ArchRProject.

This function will add total counts of scATAC cells in provided features into ArchRProject.

addFeatureCounts(
  ArchRProj = NULL,
  features = NULL,
  name = NULL,
  addRatio = TRUE,
  threads = getArchRThreads(),
  logFile = createLogFile("addFeatureCounts")
)

Arguments

ArchRProj

An ArchRProject object.

features

A GRanges object of features to count scATAC-seq data in.

name

A character defining the name of the features. "nameCounts" and "nameRatio" will be added to the ArchRProject.

addRatio

A boolean indicating whether to add the "nameRatio" to the ArchRProject.

threads

The number of threads to use for parallel execution.

logFile

The path to a file to be used for logging ArchR output.

Examples

# Get Test ArchR Project
proj <- getTestProject()

# Add Feature Counts
proj <- addFeatureCounts(proj, features = getPeakSet(proj), name = 'ReadsInPeaks')