Import gene ontology (GO) terms per gene name — goTermsPerGeneName • AcidGenomes

Import gene ontology (GO) terms per gene name

Usage

goTermsPerGeneName(
  organism,
  geneNames = NULL,
  format = c("long", "split", "nested")
)

Arguments

organism: character(1). Full Latin organism name (e.g. "Homo sapiens").
geneNames: character or NULL. Return specific genes, or when NULL, return all genes.
format: character(1). Return GO terms in "long", "split", or "nested" formats. Processing GO terms into nested format is CPU intensive, and is recommended to set geneNames in this case.

Value

Varies, depending on format argument.

"long": DFrame with "geneName", "goCategory", "goId", and "goName" columns.
"split": SplitDFrameList: Split by geneName column. Contains "geneName", "goCategory", "goId", and "goName" columns.
"nested": DFrame with "geneName", "goBp", "goCc", and "goMf" columns. Does not contain any duplicates in "geneName" column.

Note

Updated 2023-12-15.

See also

http://current.geneontology.org/products/pages/downloads.html
https://www.ebi.ac.uk/GOA/
https://geneontology.org/docs/go-annotation-file-gaf-format-2.2/
https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz
Python goatools package.

Examples

object <- goTermsPerGeneName(organism = "Homo sapiens", format = "long")
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'con' in selecting a method for function 'import': formal argument "USE.NAMES" matched by multiple actual arguments
print(object)
#> Error: object 'object' not found