Description Usage Arguments Value Examples
Read a GO annotation file in GPA format. Further information about the GPA format is available from the Gene Ontology Consortium.
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filepath |
the location of the GPA file. Files can be downloaded from ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/ |
database |
optionally, provide a Bioconductor 'AnnotationDbi' database to map identifiers from UniProt to some other accession |
accession |
optionally, the type of identifier to map UniProt accessions to using a Bioconductor 'AnnotationDbi' database. Must be a keytype in the database. |
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. |
propatate |
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 GPA file
1 2 3 4 5 6 | # read human GOA and map to Ensembl, filtering IEA annotations
go <- read_gpa("goa_human.gpa.gz", database = org.Hs.eg.db,
accession = "ENSEMBL", filter.evidence = "IEA")
# read mouse GOA and map to gene symbol, filtering IEA and IPI annotations
go <- read_gpa("goa_mouse.gpa.gz", database = org.Mm.eg.db,
accession = "SYMBOL", filter.evidence = c("IEA", "IPI"))
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