getFragmentsFromProject: Get the fragments from an ArchRProject
In haibol2016/ArchR_debug: Analyzing single-cell regulatory chromatin in R.

getFragmentsFromProject

R Documentation

Get the fragments from an ArchRProject

Description

This function retrieves the fragments from a given ArchRProject as a GRangesList object.

Usage

getFragmentsFromProject(
  ArchRProj = NULL,
  subsetBy = NULL,
  cellNames = NULL,
  verbose = FALSE,
  logFile = createLogFile("getFragmentsFromProject")
)

Arguments

`subsetBy`	A Genomic Ranges object to subset fragments by.
`cellNames`	A character vector indicating the cell names of a subset of cells from which fragments whould be extracted. This allows for extraction of fragments from only a subset of selected cells. By default, this function will extract all cells from the provided ArrowFile using `getCellNames()`.
`verbose`	A boolean value indicating whether to use verbose output during execution of this function. Can be set to `FALSE` for a cleaner output.
`logFile`	The path to a file to be used for logging ArchR output.
`ArchRProject`	An `ArchRProject` object to get fragments from.