annotation_enrichment_analysis: Perform enrichment analysis

In VoisinneG/pannot: Annotate and perform annotation enrichment analysis within sets of proteins or genes

Perform enrichment analysis

Description

Perform enrichment analysis using a hypergeometric test for protein annotations stored in a formatted data.frame

Usage

annotation_enrichment_analysis(
  df,
  sep_split = "|",
  sep = NULL,
  idx_subset,
  annotation_selected = names(df)[2],
  col_names = names(df)[1],
  two_sided = FALSE,
  updateProgress = NULL,
  showProgress = TRUE,
  orderOutput = TRUE
)

Arguments

df	a data.frame with annotations corresponding to each row. Types of annotations are organized by columns. For a given type of annotations, annotations are separated by sep.
sep_split	Character string separating different annotation groups.
sep	Character string separating different annotations.
idx_subset	indexes of the foreground set.
annotation_selected	set of annotations on which to perform the analysis. Annotations selectd must be a subset of df's names.
col_names	df's column name containing gene names.
two_sided	logical, perform a two-sided hypergeometric test
updateProgress	logical, function to show progress in shiny app
showProgress	logical, show progress in console
orderOutput	logical, order annotations by enrichment p-values in the output data.frame

Value

a data.frame

VoisinneG/pannot documentation built on July 5, 2023, 4:19 p.m.