Helper function to generate fgsea simple-based permutations

Helper function to generate fgsea simple-based permutations

Usage

rs_calc_gsea_stat_cumulative_batch(
  stats,
  pathway_scores,
  pathway_sizes,
  iters,
  gsea_param,
  return_add_stats,
  seed
)

Arguments

stats

Numeric vector. The gene level statistic. Needs to sorted in descending nature.

pathway_scores

Numeric vector. The enrichment scores for the pathways

pathway_sizes

Integer vector. The sizes of the pathways.

iters

Integer. Number of permutations.

gsea_param

Float. The Gene Set Enrichment parameter.

return_add_stats

Boolean. Returns additional statistics necessary for the multi-level calculations.

seed

Integer. For reproducibility purposes

Value

List with the following elements

• es Enrichment scores for the gene sets

• nes Normalised enrichment scores for the gene sets

• pvals The calculated p-values.

• n_more_extreme Number of times the enrichment score was bigger or smaller than the permutation (pending sign).

• size Pathway size.

If return_add_stats is set to true, there is additional elements in the list:

• le_zero Number of times the permutation was less than zero.

• ge_zero Number of times the permutation was greater than zero.