addFeatureMatrix: Add a feature matrix to an ArchRProject or a set of...
In haibol2016/ArchR_debug: Analyzing single-cell regulatory chromatin in R.

addFeatureMatrix

R Documentation

Add a feature matrix to an ArchRProject or a set of ArrowFiles

Description

This function for each sample will independently compute counts for each feature per cell in the provided ArchRProject or set of ArrowFiles.

Usage

addFeatureMatrix(
  input = NULL,
  features = NULL,
  matrixName = "FeatureMatrix",
  ceiling = 10^9,
  binarize = FALSE,
  verbose = TRUE,
  threads = getArchRThreads(),
  parallelParam = NULL,
  force = TRUE,
  logFile = createLogFile("addFeatureMatrix")
)

Arguments

`input`	An `ArchRProject` object or character vector of paths to ArrowFiles.
`features`	A `GRanges` object containing the regions (aka features) to use for counting insertions for each cell.
`matrixName`	The name to be used for storage of the feature matrix in the provided `ArchRProject` or ArrowFiles.
`ceiling`	The maximum counts per feature allowed. This is used to prevent large biases in feature counts.
`binarize`	A boolean value indicating whether the feature matrix should be binarized prior to storage. This can be useful for downstream analyses when working with insertion counts.
`verbose`	A boolean value that determines whether standard output includes verbose sections.
`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 matrix indicated by `matrixName` to be overwritten if it already exists in the `input`.
`logFile`	The path to a file to be used for logging ArchR output.