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Add HMMCopy results to sce object

Source: R/hmmcopy_utils.R
add_hmmcopy.Rd

Add HMMCopy results to sce object

Usage

add_hmmcopy(
  sce,
  verbose = FALSE,
  ncores = 1,
  assay_name = paste0("counts_gc_", sce@metadata$gc_cor_method),
  save_raw_hmm = NULL,
  slot_suffix = NULL,
  ...
)

Arguments

sce

an SCE object

verbose

Message verbosity

ncores

Number of cores

assay_name

Name of the assay with counts to input into HMMcopy. Ideally these are GC corrected.

save_raw_hmm

Path to save raw hmm data in an rda file

slot_suffix

Suffix to add to newly created copy and state assay slots.

...

Additional parameters to pass to run_sc_hmmcopy(), such as param

Value

an sce object with hmm copy metadata added to coldata, and new slots copy and state