do GSEA

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

Value

enriched_result

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".

See also

fgsea::fgsea