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Import gene ontology (GO) terms per gene name

Source: R/goTermsPerGeneName.R
goTermsPerGeneName.Rd

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")
#> → Caching URL at <https://geneontology.org/gene-associations/goa_human.gaf.gz> into /private/var/folders/pt/1g5629f1699dfjwdfh32q50m0000gn/T/koopa-r-docs-build-l3dklp41/home/.cache/R/AcidGenomes/BiocFileCache.
#> 
#> → Importing /private/var/folders/pt/1g5629f1699dfjwdfh32q50m0000gn/T/Rtmpl5LqT9/yLwkQMlg24-17904180853212/pipette-a36567baca93.gaf using base::`read.table()`.
#> → Caching URL at <https://purl.obolibrary.org/obo/go/go-basic.obo> into /private/var/folders/pt/1g5629f1699dfjwdfh32q50m0000gn/T/koopa-r-docs-build-l3dklp41/home/.cache/R/AcidGenomes/BiocFileCache.
#> 
print(object)
#> DataFrame with 337621 rows and 4 columns
#>                    geneName  goCategory        goId                 goName
#>                 <character> <character> <character>            <character>
#> 1      19s-20s-pa28ab_human          BP  GO:0006979 response to oxidativ..
#> 2      19s-20s-pa28ab_human          BP  GO:0061136 regulation of protea..
#> 3      19s-20s-pa28ab_human          BP  GO:0071357 cellular response to..
#> 4      19s-20s-pa28ab_human          CC  GO:0005829                cytosol
#> 5      19s-20s-pa28ab_human          MF  GO:0004298 threonine-type endop..
#> ...                     ...         ...         ...                    ...
#> 337617         znt8_human-1          MF  GO:0005385 zinc ion transmembra..
#> 337618         znt8_human-1          MF  GO:0008270       zinc ion binding
#> 337619         znt8_human-1          MF  GO:0015297    antiporter activity
#> 337620   zyg11b-elobc_human          BP  GO:0043161 proteasome-mediated ..
#> 337621   zyg11b-elobc_human          MF  GO:0061630 ubiquitin protein li..