Add TileMatrix to ArrowFiles or an ArchRProject

This function, for each sample, will independently compute counts for each tile

addTileMatrix(
  input = NULL,
  chromSizes = if (inherits(input, "ArchRProject")) getChromSizes(input) else NULL,
  blacklist = if (inherits(input, "ArchRProject")) getBlacklist(input) else NULL,
  tileSize = 500,
  binarize = TRUE,
  excludeChr = c("chrM", "chrY"),
  threads = getArchRThreads(),
  parallelParam = NULL,
  force = FALSE,
  logFile = createLogFile("addTileMatrix")
)

Arguments

input

An ArchRProject object or character vector of ArrowFiles.

chromSizes

A named numeric vector containing the chromsome names and lengths. The default behavior is to retrieve this from the ArchRProject using getChromSizes().

blacklist

A GRanges object containing genomic regions to blacklist counting in these tiles. The default behavior is to retrieve this from the ArchRProject using getBlacklist().

tileSize

The size of the tiles used for binning counts in the "TileMatrix".

binarize

A boolean value indicating whether the "TileMatrix" should be binarized prior to storage.

excludeChr

A character vector containing the seqnames of the chromosomes that should be excluded from the "TileMatrix".

threads

The number of threads to be used for parallel computing.

parallelParam

A list of parameters to be passed for biocparallel/batchtools parallel computing.

force

A boolean value indicating whether to force the "TileMatrix' to be overwritten if it already exist in the given input.

logFile

The path to a file to be used for logging ArchR output.

Examples

# Get Test ArchR Project
proj <- getTestProject()

# Add Tile Matrix
proj <- addTileMatrix(proj, force = TRUE, tileSize = 25000)