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Run GO enrichment with elimination with fgsea simple

fgsea_simple_go_elim.Rd

This method takes the GeneOntologyElim and a vector of gene level statistics to perform fgsea (simple) leveraging ontological information. It starts at the lowest levels of the ontology and tests if there is significant enrichment for any GO terms. If the threshold of the p-value is below the elimination threshold, the genes from this term will be removed from all its ancestors. The function then proceeds to the next level of the ontology and repeats the process.

Usage

fgsea_simple_go_elim(
  object,
  stats,
  elim_threshold = 0.05,
  nperm = 2000L,
  gsea_params = params_gsea(max_size = 2000L),
  seed = 42L
)

Arguments

object

The underlying class, see GeneOntologyElim().

stats

Named numeric vector. The gene level statistic.

elim_threshold

Float. Threshold from which p-value onwards the elimination on the ancestors shall be conducted.

nperm

Integer. Number of permutation tests. Defaults to 2000L

gsea_params

List. The GSEA parameters, see params_gsea() wrapper function. This function generates a list containing:

  • min_size - Integer. Minimum size for the gene sets.

  • max_size - Integer. Maximum size for the gene sets.

  • gsea_param - Float. The GSEA parameter. Defaults to 1.0.

  • sample_size - Integer. Number of samples to iterate through for the multi-level implementation of fgsea.

  • eps - Float. Boundary for calculating the p-value. Used for the multi- level implementation of fgsea.

seed

Random seed for reproducibility.

Value

data.table with enrichment results.