getPopFrags {MOCHA}

Extract fragments by populations from an ArchR Project

Description

getPopFrags returns a list of sample-specific fragments per cell population as a GRangesList.

Usage

getPopFrags(
  ArchRProj,
  cellPopLabel,
  cellSubsets = "ALL",
  poolSamples = FALSE,
  numCores = 1,
  verbose = FALSE
)

Arguments

ArchRProj

The ArchR Project.

cellPopLabel

The name of the metadata column of the ArchR Project that contains the populations of cells you want to extract fragments from.

cellSubsets

Default is 'ALL'. If you want to export only some populations, then give it a list of group names. This needs to be unique - no duplicated names. This list of group names must be identical to names that appear in the given cellPopLabel metadata column of the ArchR Project.

poolSamples

Set TRUE to pool sample-specific fragments by cell population. By default this is FALSE and sample-specific fragments are returned.

numCores

Number of cores to use.

verbose

Set TRUE to display additional messages. Default is FALSE.

Value

A list of GRanges containing fragments. Each GRanges corresponds to a population defined by cellSubsets and sample.