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Generates a new ADTCounts class

new_adt_counts_clr.Rd

This function generates a new ADTCounts class which uses CLR normalisation under the hood. You have the choice between Seurat-style CLR (no negative values) and normal CLR (allows negative values).

Usage

new_adt_counts_clr(
  raw_counts,
  cell_info,
  seurat_clr = FALSE,
  clean_clr_counts = TRUE,
  percentile = 0.01
)

Arguments

raw_counts

Numeric matrix. The raw ADT counts.

cell_info

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

seurat_clr

Boolean. Shall a Seurat-style CLR be applied.

clean_clr_counts

Boolean. Shall the per-protein 1st percentile be removed from the CLR normalised counts.

percentile

Numeric. The percentile to remove to reduce background effects.

Value

ADTCounts that contains the raw and normalised ADT counts.

Examples

# CLR normalisation of synthetic ADT counts
adt <- generate_single_cell_test_data_adt()
cell_info <- stats::setNames(
  seq_len(nrow(adt$counts)),
  rownames(adt$counts)
)
new_adt_counts_clr(adt$counts, cell_info = cell_info)
#> ADTCounts
#>   Cells:     1000 
#>   Proteins:  15 
#>   Type:      CLR