addTileMatrix: Add TileMatrix to ArrowFiles or an ArchRProject
In haibol2016/ArchR_debug: Analyzing single-cell regulatory chromatin in R.

addTileMatrix

R Documentation

Add TileMatrix to ArrowFiles or an ArchRProject

Description

This function, for each sample, will independently compute counts for each tile per cell in the ArrowFile

Usage

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.