addFeatureMatrix: Add a feature matrix to an ArchRProject or a set of...

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

Add a feature matrix to an ArchRProject or a set of ArrowFiles

Description

This function for each sample will independently compute counts for each feature per cell in the provided ArchRProject or set of ArrowFiles.

Usage

addFeatureMatrix(
  input = NULL,
  features = NULL,
  matrixName = "FeatureMatrix",
  ceiling = 10^9,
  binarize = FALSE,
  verbose = TRUE,
  threads = getArchRThreads(),
  parallelParam = NULL,
  force = TRUE,
  logFile = createLogFile("addFeatureMatrix")
)

Arguments

input	An ArchRProject object or character vector of paths to ArrowFiles.
features	A GRanges object containing the regions (aka features) to use for counting insertions for each cell.
matrixName	The name to be used for storage of the feature matrix in the provided ArchRProject or ArrowFiles.
ceiling	The maximum counts per feature allowed. This is used to prevent large biases in feature counts.
binarize	A boolean value indicating whether the feature 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 matrix indicated by matrixName to be overwritten if it already exists in the input.
logFile	The path to a file to be used for logging ArchR output.

Examples

# Get Test ArchR Project
proj <- getTestProject()

# Add Custom Matrix Which Is Just Peak Set
proj <- addFeatureMatrix(proj, features = getPeakSet(proj))

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