getFootprints: Calculate footprints from an ArchRProject

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

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.

Examples

# Get Test ArchR Project
proj <- getTestProject()

# Get Motif Positions
positions <- getPositions(proj)

# Get Footprints
seFoot <- getFootprints(ArchRProj = proj, positions = positions, groupBy = "Clusters", minCells = 10)

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