Calculate the proportions of reads for specific gene sets — gene_set_proportions

This is a helper function that calculates proportions of reads belonging to given gene sets. This can be used for example for the calculation of percentage mitochondrial reads per cell. These will be automatically added to the obs table

Usage

gene_set_proportions_sc(
  object,
  gene_set_list,
  streaming = NULL,
  .verbose = TRUE
)

Arguments

object: SingleCells class.
gene_set_list: A named list with each element containing the gene identifiers of that set. These should be the same as get_gene_names(object)!
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

# read proportion of a gene set, the mitochondrial percentage pattern
sc <- demo_single_cells(prepped = FALSE)
sc <- gene_set_proportions_sc(
  sc,
  gene_set_list = list(set_a = c("gene_01", "gene_02", "gene_03")),
  .verbose = FALSE
)
head(unlist(sc[["set_a"]]))
#>      set_a1      set_a2      set_a3      set_a4      set_a5      set_a6 
#> 0.161870509 0.021021022 0.016949153 0.283667624 0.000000000 0.009070295 

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