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Score gene sets against a calibrated blitzGSEA null

rs_blitzgsea_score.Rd

[Experimental]

Each gene set costs one enrichment score plus one gamma tail evaluation. The gene sets are expected to have been filtered to the desired size bounds and intersected with the signature already.

Usage

rs_blitzgsea_score(stats, pathways, null_model, blitz_params)

Arguments

stats

Numeric vector. The gene level statistic. Needs to be sorted in descending nature and be the same signature the null was calibrated on.

pathways

List. One integer vector of index positions per gene set, indexed to R's 1-indexing. Order and duplicates do not matter.

null_model

List. The calibrated null from rs_blitzgsea_calibrate().

blitz_params

List. The blitzGSEA parameters, see params_blitzgsea(). Only centre is read here and it has to match what the calibration used.

Value

List with the following elements

  • es Numeric vector. Enrichment scores for the gene sets.

  • nes Numeric vector. Normalised enrichment scores.

  • pvals Numeric vector. Two-sided p-values from the gamma approximation.

  • sidak Numeric vector. Sidak-adjusted p-values.

  • fdr Numeric vector. Benjamini-Hochberg adjusted p-values.

  • size Integer vector. Gene set size after intersection.

  • leading_edge List of integer vectors with the leading edge index positions, indexed to R's 1-indexing.