get_GO_list_from_ontologies_with_evidence_codes: get_GO_list_from_ontologies_with_evidence_codes

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.

Usage

get_GO_list_from_ontologies_with_evidence_codes(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.

Value

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

Examples

Human_trim_GO <- get_GO_list_from_ontologies_with_evidence_codes('hsapiens')
summary(Human_trim_GO[1:5])

VCCRI/XGSA documentation built on May 9, 2019, 9:41 p.m.