reduce_genesets: Reduce the set of significant genesets to a minimum

In goat: Gene Set Analysis Using the Gene Set Ordinal Association Test

Reduce the set of significant genesets to a minimum

Description

Analyses are performed independently per 'source' of genesets. The result of this function is the geneset table with a newly appended column 'signif_and_reduced'

Usage

reduce_genesets(
  clusters,
  simscore_threshold = 0.9,
  universe_fraction = 0.25,
  signifgenes_fraction = 0.9
)

Arguments

clusters	results from cluster_genesets()
simscore_threshold	similarity score (0~1) that is required to consider one geneset to be a "parent term" of another. Setting a lower value will yield fewer genesets / stronger summarization. Typical settings for this parameter are 0.8~0.99 (0.9 is default)
universe_fraction	discard genesets that cover more than X fraction of all genes in the universe (unique set of genes covered by all significant genesets). Setting this to 0.25 will deprioritize genesets that cover 25% of all genes (in significant genesets). This prevents very generic GO terms like "protein-containing complex" to be included in results. Typical settings for this parameter are 0.1~0.5 (0.25 is default)
signifgenes_fraction	the minimum fraction of "foreground genes" ('genes_signif' column) found across all significant genesets that should be covered by the reduced geneset collection. This parameter doesn't do anything if there are fewer than 5 "foreground genes" alltogether. Typical settings for this parameter are 0.75~0.95 (0.9 is default)

Value

the genesets table from the clusters parameter, with results in column "signif_and_reduced"

goat documentation built on Aug. 27, 2025, 5:12 p.m.