exportPeakMatrixForSTREAM: Get a PeakMatrix stored in an ArchRProject and write out for...

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

Get a PeakMatrix stored in an ArchRProject and write out for STREAM

Description

This function gets a PeakMatrix from an ArchRProject and writes it to a set of files for STREAM (https://github.com/pinellolab/STREAM)

Usage

exportPeakMatrixForSTREAM(
  ArchRProj = NULL,
  useSeqnames = NULL,
  verbose = TRUE,
  binarize = FALSE,
  threads = getArchRThreads(),
  logFile = createLogFile("exportMatrixForSTREAM")
)

Arguments

ArchRProj	An ArchRProject object to get data matrix from.
useSeqnames	A character vector of chromosome names to be used to subset the data matrix being obtained.
verbose	A boolean value indicating whether to use verbose output during execution of this function. Can be set to FALSE for a cleaner output.
binarize	A boolean value indicating whether the matrix should be binarized before return. This is often desired when working with insertion counts.
logFile	The path to a file to be used for logging ArchR output.

Examples

# Get Test ArchR Project
proj <- getTestProject()

# Export Matrix For Stream
exportPeakMatrixForSTREAM(proj)

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