addPeakMatrix: Add a Peak Matrix to the ArrowFiles of an ArchRProject

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

Add a Peak Matrix to the ArrowFiles of an ArchRProject

Description

This function, for each sample, will independently compute counts for each peak per cell in the provided ArchRProject using the "PeakMatrix".

Usage

addPeakMatrix(
  ArchRProj = NULL,
  ceiling = 4,
  binarize = FALSE,
  verbose = TRUE,
  threads = getArchRThreads(),
  parallelParam = NULL,
  force = TRUE,
  logFile = createLogFile("addPeakMatrix")
)

Arguments

ArchRProj	An ArchRProject object.
ceiling	The maximum counts per feature allowed. This is used to prevent large biases in peak counts.
binarize	A boolean value indicating whether the peak matrix should be binarized prior to storage. This can be useful for downstream analyses when working with insertion counts.
verbose	A boolean value that determines whether standard output includes verbose sections.
threads	The number of threads to be used for parallel computing.
parallelParam	A list of parameters to be passed for biocparallel/batchtools parallel computing.
force	A boolean value indicating whether to force the "PeakMatrix" to be overwritten if it already exist in the given ArchRProject.
logFile	The path to a file to be used for logging ArchR output.

Examples

# Get Test ArchR Project
proj <- getTestProject()

# Add Peak Matrix
proj <- addPeakMatrix(proj)

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