get_GO: get_GO

In VCCRI/XGSA: XGSA: A statistical method for cross-species gene set analysis

Description

This function retrieves GO mappings with only the supplied evidence codes and from only the supplied ontologies and converts the result into a list. It retrieves the full and redundant GO mappings.

Usage

get_GO(species, evidence.codes = c("EXP", "IDA", "IPI", "IMP", "IGI", "IEP",
  "TAS", "IC"), ontologies = c("biological_process", "molecular_function",
  "cellular_component"))

Arguments

species	Species name in the form 'hsapiens'
evidence.codes	A character vector of evidence codes, defaults to 'direct' evidence = c("EXP","IDA","IPI","IMP","IGI","IEP", "TAS", "IC"). A description of GO evidence codes can be found here: http://geneontology.org/page/guide-go-evidence-codes
ontologies	A character vector of the desired ontologies to query, defaults to all three of them - i.e. c("biological_process", "molecular_function", "cellular_component")

Details

This function retrieves GO mappings with only the supplied evidence codes and from only the supplied ontologies and converts the result into a list. It retrieves the full and redundant GO mappings.

Value

This function returns a named list of GO terms with annotated Ensembl gene IDs within each element.

Examples

Human_full_GO <- get_GO('hsapiens')

VCCRI/XGSA documentation built on March 5, 2021, 10:22 p.m.