Add ADT counts to SingleCellsMultiModal

This method allows you to add ADT counts to a SingleCellsMultiModal. Assumes the transcriptomics data has already been ingested and the cells to keep are known. The method subsets the ADT counts to the kept cells, applies the requested normalisation (CLR or DSB), populates the "var_adt" table in the DuckDB, and attaches an ADTCounts to the class.

Usage

add_adt_counts_sc(object, adt_counts, method = c("clr", "dsb"), ...)

Arguments

object

SingleCellsMultiModal class.

adt_counts

Numeric matrix. Cells x features matrix of raw ADT counts.

method

String. One of c("clr", "dsb"). Normalisation method.

...

Additional arguments forwarded to the normalisation constructor. For method = "clr": seurat_clr, clean_clr_counts, percentile. For method = "dsb": empty_drops, isotype_names, dsb_params, scale_factor, seed, verbose. See new_adt_counts_clr() and new_adt_counts_dsb().

Value

Returns a SingleCellsMultiModal with the ADT data added.

Examples

# a CLR-normalised ADT layer on top of an ingested RNA modality
rna <- generate_single_cell_test_data()
adt <- generate_single_cell_test_data_adt()
dir <- tempfile("bixverse_mm")
dir.create(dir)
object <- load_r_data(
  SingleCellsMultiModal(dir_data = dir),
  counts = rna$counts,
  obs = rna$obs,
  var = rna$var,
  sc_qc_param = params_sc_min_quality(min_unique_genes = 5L),
  .verbose = FALSE
)
object <- add_adt_counts_sc(object, adt_counts = adt$counts, method = "clr")
get_adt_names(object)
#>  [1] "protein_01" "protein_02" "protein_03" "protein_04" "protein_05"
#>  [6] "protein_06" "protein_07" "protein_08" "protein_09" "protein_10"
#> [11] "protein_11" "protein_12" "protein_13" "protein_14" "protein_15"

unlink(dir, recursive = TRUE, force = TRUE)