GSEA_permut_R: Compute ES scores for Gene Set Enrichment Analysis (GSEA)...

In lusystemsbio/NetAct: NetAct -- a computational platform to construct core transcription factor regulatory networks using gene activity

Compute ES scores for Gene Set Enrichment Analysis (GSEA) with a new permutation method (using the original GSEA algorithm)

Description

The function uses the original GSEA enrichment score calculation but using the new permutation method. Here, the gene symbols/names are permutated without changing the ranking vector (stats_vector).

Usage

GSEA_permut_R(sim_all, gs, stats_vector)

Arguments

sim_all	a matrix of permutated gene lists
gs	a vector of genes in the gene set
stats_vector	a vector of DEG statistics for every gene in gene_list (rank_vector in the DEG results) Absolute values of the t-statistics are required for the desired performance.

Value

tmp_sim_sgeas: a vector of ES values for all permutated gene lists

lusystemsbio/NetAct documentation built on Sept. 7, 2024, 8:34 p.m.