projectBulkATAC: Project Bulk ATAC-seq data into single cell subspace

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

Project Bulk ATAC-seq data into single cell subspace

Description

This function will Project Bulk ATAC-seq data into single cell subspace.

Usage

projectBulkATAC(
  ArchRProj = NULL,
  seATAC = NULL,
  reducedDims = "IterativeLSI",
  embedding = "UMAP",
  n = 250,
  verbose = TRUE,
  threads = getArchRThreads(),
  force = FALSE,
  logFile = createLogFile("projectBulkATAC")
)

Arguments

ArchRProj	An ArchRProject object containing the dimensionality reduction matrix passed by reducedDims.
seATAC	A SummarizedExperiment object containing bulk ATAC-seq data.
reducedDims	A string specifying the name of the reducedDims object to be used.
embedding	A string specifying the name of the embedding object to be used.
n	An integer specifying the number of subsampled "pseudo single cells" per bulk sample.
verbose	A boolean value indicating whether to use verbose output during execution of this function. Can be set to FALSE for a cleaner output.
threads	The number of threads used for parallel execution
force	A boolean value indicating whether to force the projection of bulk ATAC data even if fewer than 25% of the features are present in the bulk ATAC data set.
logFile	The path to a file to be used for logging ArchR output.

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