addFeatureCounts: This function will add total counts of scATAC cells in...

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

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

Description

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

Usage

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')

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