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Calculate the proportions of reads for the Top N genes

top_genes_perc_sc.Rd

This is a helper function that calculates proportions of reads to the Top N genes by expression in a given cell. High values here can indicate low complexity, quality cells. The values will be automatically added to the obs table.

Usage

top_genes_perc_sc(
  object,
  top_n_vals = c(25L, 50L, 100L),
  streaming = NULL,
  .verbose = TRUE
)

Arguments

object

SingleCells class.

top_n_vals

Integer. The Top N thresholds to test.

streaming

Optional Boolean. Shall the data be streamed in. Useful for larger data sets where you wish to avoid loading in the whole data. If NULL, will automatically detect.

.verbose

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

Value

It will add the columns based on the names in the gene_set_list to the obs table.

Examples

# share of a cell's reads taken by its top 5 and top 10 genes
sc <- demo_single_cells(prepped = FALSE)
sc <- top_genes_perc_sc(sc, top_n_vals = c(5L, 10L), .verbose = FALSE)
head(unlist(sc[["top_5_genes_percentage"]]))
#> top_5_genes_percentage1 top_5_genes_percentage2 top_5_genes_percentage3 
#>               0.5863310               0.6096096               0.6924940 
#> top_5_genes_percentage4 top_5_genes_percentage5 top_5_genes_percentage6 
#>               0.7106017               0.6787879               0.7664399 

unlink(sc@dir_data, recursive = TRUE, force = TRUE)