run_gsea: Performs gene set enrichment analysis with fgsea on a table...
In broadinstitute/cdsr_gsea: CDS function for gene set enrichment analysis

Description Usage Arguments Value

View source: R/gsea_functions.R

Performs gene set enrichment analysis with fgsea on a table of gene stats

run_gsea(
  gene_stats,
  term2gene,
  gene_var = "Gene",
  rank_var = "logFC",
  dir = "both",
  method = "fgsea",
  min_size = 1,
  max_size = 500
)

`gene_stats`	a table of gene level stats.
`term2gene`	a table of gene_sets in term2gene format.
`gene_var`	name of the column containing gene names.
`rank_var`	name of the column containing gene stats.
`dir`	direction(s) to consider. Options are ("both","pos","neg")
`method`	GSEA methods. Options are ("fgsea").
`min_size`	minimal size of a gene set to test.
`max_size`	maximal size of a gene set to test. Defaults to 500.

A table with the following columns:

term: gene set name.
p_value: enrichment p-value.
p_adjust: BH-adjusted p-value.
ES: enrichment score.
NES: enrichment score normalized to mean enrichment of random samples of the same size.
direction: enrichment direction. Options are ("both","pos","neg").
size: size of the gene set.
leading_edge: vector with indexes of leading edge genes that drive the enrichment.

broadinstitute/cdsr_gsea documentation built on Sept. 1, 2020, 5:39 a.m.