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Add GC correction to SCE Object

Source: R/gc_correction.R
add_gc_cor.Rd

Add GC correction to SCE Object

Usage

add_gc_cor(
  sce,
  gc = SummarizedExperiment::rowData(sce)$gc,
  assay_name = "counts",
  method = c("modal", "copykit", "loess"),
  verbose = FALSE,
  bpparam,
  ...
)

Arguments

sce

an SCE object

gc

GC corresponding to bins (rows) in the matrix

assay_name

Name of assay on which to perform GC correction

method

Specifies the type of GC correction to perform. One of 'modal', 'copykit', or 'loess'

verbose

Message verbosity (TRUE/FALSE)

bpparam

BiocParallel params

...

Additional arguments to be passed to GC correction methods

Value

sce object with corrected GC count matrix in assay(sce, 'counts_gc_[method]'). See perform_gc_cor for more information.