exportPeakMatrixForSTREAM: Get a PeakMatrix stored in an ArchRProject and write out for...
In GreenleafLab/ArchR: Analyzing single-cell regulatory chromatin in R.

exportPeakMatrixForSTREAM

R Documentation

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.