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Helper function to generate traditional GSEA-based permutations

rs_calc_gsea_stat_traditional_batch.Rd

Helper function to generate traditional GSEA-based permutations

Usage

rs_calc_gsea_stat_traditional_batch(
  stats,
  pathway_scores,
  pathway_sizes,
  iters,
  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.

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.