simplify_enrichment_results: Simplifies enrichment data frame by overlap between...

In nicohuttmann/pOmics: Framework for proteomics data analysis

Simplifies enrichment data frame by overlap between annotations, semantic similarity for GO terms and minimum protein count

Description

Simplifies enrichment data frame by overlap between annotations, semantic similarity for GO terms and minimum protein count

Usage

simplify_enrichment_results(
  enrichment_df,
  by.overlap = T,
  overlap.threshold = 0.7,
  separator = ";",
  by.semantic = F,
  similarity.measure = "Wang",
  similarity.threshold = 0.4,
  dataset,
  overlap.first = T,
  minimum.count = 0
)

Arguments

enrichment_df
by.overlap	use simplify_set_overlap
overlap.threshold	minimum fraction of common proteins in protein set with lower p-value to be excluded
separator	string separator of proteins
by.semantic	use simplify_GO_terms_semantic
similarity.measure	method to measure pairwise GO terms similarity (see ?GOSemSim::mgoSim)
similarity.threshold	threshold to remove terms (0-1, default = 0.4)
dataset	dataset
minimum.count	number of proteins per annotation

nicohuttmann/pOmics documentation built on Sept. 21, 2022, 9:28 a.m.