gsea_feature_enrichment: do GSEA

In rmflight/categoryCompare2: Meta-Analysis of High-Throughput Experiments Using Feature Annotations

do GSEA

Description

Performs gene-set enrichment analysis using the 'fgsea' package.

Usage

gsea_feature_enrichment(
  gsea_features,
  min_features = 15,
  max_features = 500,
  return_type = "cc2",
  ...
)

Arguments

gsea_features	a GSEA features object
min_features	the minimum number of features for an annotation (default = 15)
max_features	the maximum number of features for an annotation (default = 500)
return_type	what type of object should be returned? ("cc2" or "fgsea")
...	other 'fgsea' options

Details

The runtime is dependent on the maximum size of the provided annotation, so the authors of 'fgsea' recommend a maximum size of 500. In addition, to calculate statistics, a minimum size of annotated features are required. Going below 15 may not be advised. If you want to use other 'fgsea' functions, it is recommended to set 'return_type = "fgsea"'. Otherwise, you should keep the default of "cc2".

Value

enriched_result

See Also

fgsea::fgsea

rmflight/categoryCompare2 documentation built on Dec. 18, 2024, 9:13 a.m.