read_gaf: Read a GAF file
In fosterlab/CFTK: The Co-Fractionation Toolkit

Description Usage Arguments Value Examples

Read a GO annotation file in GAF format. Further information about the GAF format is available from the Gene Ontology Consortium.

read_gaf(
  filepath,
  filter_NOT = TRUE,
  filter_evidence = NULL,
  ontology = NULL,
  propagate = TRUE
)

`filepath`	the location of the GAF file
`filter_NOT`	if true, filter annotations with the qualifier NOT
`filter_evidence`	optionally, specify evidence codes to filter. By default, evidence codes ND, IPI, IEA and NAS are filtered.
`ontology`	optionally, provide the Gene Ontology itself as an object read in by the `ontologyIndex` package from an OBO file
`propagate`	if true, and an ontology file is provided, all ancestors of a given term are associated with each protein.

a data.frame containing the filtered GAF file

# read human GOA and filtering IEA annotations
# go = read_gaf("goa_human.gaf.gz", filter_evidence = "IEA")
# read mouse GOA wthout filtering any annotations
# go = read_gaf("goa_mouse.gaf.gz", filter_evidence = NULL)

fosterlab/CFTK documentation built on Jan. 19, 2021, 10:31 p.m.