getFootprints: Calculate footprints from an ArchRProject
In haibol2016/ArchR_debug: Analyzing single-cell regulatory chromatin in R.

getFootprints

R Documentation

Calculate footprints from an ArchRProject

Description

This function will get footprints for all samples in a given ArchRProject and return a summarized experiment object that can be used for downstream analyses

Usage

getFootprints(
  ArchRProj = NULL,
  positions = NULL,
  plotName = "Plot-Footprints",
  groupBy = "Clusters",
  useGroups = NULL,
  flank = 250,
  minCells = 25,
  nTop = NULL,
  threads = getArchRThreads(),
  verbose = TRUE,
  logFile = createLogFile("getFootprints")
)

Arguments

`ArchRProj`	An `ArchRProject` object.
`positions`	A `list` or `GRangesList` of `GRanges` containing the positions to incorporate into the footprint. Each position should be stranded.
`plotName`	The prefix to add to the file name for the output PDF file containing the footprint plots.
`groupBy`	The name of the column in `cellColData` used in the `addGroupCoverages()` function for grouping multiple cells together.
`useGroups`	A character vector that is used to select a subset of groups by name from the designated `groupBy` column in `cellColData`. This limits the groups used to perform footprinting.
`flank`	The number of basepairs from the position center (+/-) to consider as the flank.
`minCells`	The minimum number of cells required in a given cell group to permit footprint generation.
`nTop`	The number of genomic regions to consider. Only the top `nTop` genomic regions based on the "score" column in the `GRanges` object will be considered for the footprint.
`threads`	The number of threads to be used for parallel computing.
`verbose`	A boolean value that determines whether standard output includes verbose sections.
`logFile`	The path to a file to be used for logging ArchR output.