Project Bulk ATAC-seq data into single cell subspace

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

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.