The objective of gene ontology (GO) is to provide controlled vocabularies for the description of the biological process, molecular function, and cellular component of gene products. This function maps existing PFAM accessions to corresponding GO terms.
pfam2go(data_pfam, pfam)
| data_pfam | a data frame containing a column with PFAM accessions |
|---|---|
| pfam | a string defining the column name where the PFAM accessions are stored. Defaults to "acc" as per output of get_hmm function. |
http://geneontology.org/external2go/pfam2go
ftp://ftp.geneontology.org/pub/go/external2go/pfam2go
A merged data frame with columns as provided in data_pfam argument and additional columns:
Character, PFAM family accession.
Character, PFAM family name.
Character, GO term name.
Character, GO term accession.
library(ragp) data(at_nsp) pfam_pred <- get_hmm(sequence = at_nsp$sequence[1], id = at_nsp$Transcript.id[1]) pfam_pred_go <- pfam2go(data_pfam = pfam_pred, pfam = "acc") pfam_pred_go#> id name acc desc clan align_start #> 1 ATCG00660.1 Ribosomal_L20 PF00453.20 Ribosomal protein L20 <NA> 3 #> 2 ATCG00660.1 Ribosomal_L20 PF00453.20 Ribosomal protein L20 <NA> 3 #> 3 ATCG00660.1 Ribosomal_L20 PF00453.20 Ribosomal protein L20 <NA> 3 #> 4 ATCG00660.1 Ribosomal_L20 PF00453.20 Ribosomal protein L20 <NA> 3 #> align_end model_start model_end ievalue cevalue bitscore reported #> 1 108 1 104 2e-32 1e-36 111.5875 TRUE #> 2 108 1 104 2e-32 1e-36 111.5875 TRUE #> 3 108 1 104 2e-32 1e-36 111.5875 TRUE #> 4 108 1 104 2e-32 1e-36 111.5875 TRUE #> Pfam_name GO_name GO_acc #> 1 Ribosomal_L20 GO:rRNA binding GO:0019843 #> 2 Ribosomal_L20 GO:translation GO:0006412 #> 3 Ribosomal_L20 GO:ribosome GO:0005840 #> 4 Ribosomal_L20 GO:structural constituent of ribosome GO:0003735