Perform GC Correction — perform_gc_cor • scatools

Performs GC correction using over a matrix of cell counts

Usage

perform_gc_cor(
  mat,
  gc,
  valid_mat = NULL,
  method = c("modal", "copykit", "loess"),
  bpparam,
  verbose = FALSE,
  ...
)

Arguments

mat: Count matrix for GC correction
gc: GC corresponding to bins (rows) in the matrix
valid_mat: Matrix of TRUE/FALSE for valid bins. If none provided defaults to all TRUE
method: Specifies the type of GC correction to perform. One of 'modal', 'copykit', or 'loess'
bpparam: BiocParallel params
verbose: Message verbosity (TRUE/FALSE)
...: Additional arguments to be passed to GC correction methods

Value

Sparse matrix of corrected counts

Details

Note: If using modal must pass results="counts" as an argument. Uses pbmcapply::pbmclapply() for parallelization.