addGroupCoverages: Add Group Coverages to an ArchRProject object
In haibol2016/ArchR_debug: Analyzing single-cell regulatory chromatin in R.

addGroupCoverages

R Documentation

Add Group Coverages to an ArchRProject object

Description

This function will merge cells within each designated cell group for the generation of pseudo-bulk replicates and then merge these replicates into a single insertion coverage file.

Usage

addGroupCoverages(
  ArchRProj = NULL,
  groupBy = "Clusters",
  useLabels = TRUE,
  minCells = 40,
  maxCells = 500,
  maxFragments = 25 * 10^6,
  minReplicates = 2,
  maxReplicates = 5,
  sampleRatio = 0.8,
  kmerLength = 6,
  threads = getArchRThreads(),
  returnGroups = FALSE,
  parallelParam = NULL,
  force = FALSE,
  verbose = TRUE,
  logFile = createLogFile("addGroupCoverages")
)

Arguments

`ArchRProj`	An `ArchRProject` object.
`groupBy`	The name of the column in `cellColData` to use for grouping multiple cells together prior to generation of the insertion coverage file.
`useLabels`	A boolean value indicating whether to use sample labels to create sample-aware subgroupings during as pseudo-bulk replicate generation.
`minCells`	The minimum number of cells required in a given cell group to permit insertion coverage file generation.
`maxCells`	The maximum number of cells to use during insertion coverage file generation.
`maxFragments`	The maximum number of fragments per cell group to use in insertion coverage file generation. This prevents the generation of excessively large files which would negatively impact memory requirements.
`minReplicates`	The minimum number of pseudo-bulk replicates to be generated.
`maxReplicates`	The maximum number of pseudo-bulk replicates to be generated.
`sampleRatio`	The fraction of the total cells that can be sampled to generate any given pseudo-bulk replicate.
`kmerLength`	The length of the k-mer used for estimating Tn5 bias.
`threads`	The number of threads to be used for parallel computing.
`returnGroups`	A boolean value that indicates whether to return sample-guided cell-groupings without creating coverages. This is used mainly in `addReproduciblePeakSet()` when MACS2 is not being used to call peaks but rather peaks are called from a TileMatrix (`peakMethod = "Tiles"`).
`parallelParam`	A list of parameters to be passed for biocparallel/batchtools parallel computing.
`force`	A boolean value that indicates whether or not to overwrite the relevant data in the `ArchRProject` object if insertion coverage / pseudo-bulk replicate information already exists.
`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.