Gene set scoring

Calculate gene set scores using the approach described in Tirosh2016

Usage

gs_score(
  gene_set = NULL,
  genes_by_cells = NULL,
  bins = NULL,
  nmark_min = 5,
  ncells_min = 5,
  k = 100,
  kmin = 50,
  verbose = FALSE,
  null_model = TRUE,
  na.rm = TRUE
)

Arguments

gene_set

gene set

genes_by_cells

real data

bins

random data

nmark_min

min number of markers

ncells_min

min number of cells

k

number of random gene set to be considered

kmin

minimim number of k

verbose

verbosity

null_model

boolean, whether to use the permutations or not

na.rm

whether to remove or not the missing values

Value

A data.frame with the following columns:

References

Tirosh2016 10.1126/science.aad0501