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Generates a new ADTCounts class via DSB normalisation

new_adt_counts_dsb.Rd

This function generates a new ADTCounts class using DSB normalisation from Mulè et al., instead of CLR. When empty_drops is provided, the per-protein background is estimated from empty droplets. Without empty_drops, the function falls back to a 2-component k-means on the log-transformed cell counts ("ModelNegativeADTnorm").

Usage

new_adt_counts_dsb(
  raw_counts,
  cell_info,
  empty_drops = NULL,
  isotype_names = NULL,
  dsb_params = params_sc_dsb(),
  scale_factor = c("standardise", "mean_subtract"),
  seed = 42L,
  .verbose = TRUE
)

Arguments

raw_counts

Numeric matrix. Cells x proteins matrix of raw ADT counts with cell barcodes as row names and protein names as column names.

cell_info

Named integer vector. Output of get_cell_info(). Defines as elements the cell indices (R-based) and as names the barcodes.

empty_drops

Optional numeric matrix. Cells x proteins matrix of empty-droplet ADT counts. If provided, used to estimate per-protein ambient background.

isotype_names

Optional string vector. Column names in raw_counts identifying isotype control proteins. Required when dsb_params$use_isotype_controls = TRUE.

dsb_params

List. Output of params_sc_dsb() with DSB parameters.

scale_factor

String. One of c("standardise", "mean_subtract"). Only used when empty_drops is provided.

seed

Integer. Random seed for k-means initialisation.

.verbose

Boolean or integer. Controls verbosity and returns run times. FALSE -> quiet, TRUE or 1L -> normal verbosity, 2L -> detailed verbosity.

Value

ADTCounts containing the raw counts and the DSB-normalised counts.

References

Mulè et al., Nat Commun, 2022

Examples

# DSB without empty droplets, i.e. the k-means fallback, using the isotypes
adt <- generate_single_cell_test_data_adt()
cell_info <- stats::setNames(
  seq_len(nrow(adt$counts)),
  rownames(adt$counts)
)
new_adt_counts_dsb(
  adt$counts,
  cell_info = cell_info,
  isotype_names = adt$var$protein_id[adt$var$is_isotype],
  .verbose = FALSE
)
#> ADTCounts
#>   Cells:     1000 
#>   Proteins:  15 
#>   Type:      DSB