org.Sc.sgdPFAM {org.Sc.sgd.db} | R Documentation

## Map Entrez Gene IDs to Pfam IDs

### Description

org.Sc.sgdPFAM is an R object that provides mappings between an entrez gene identifier and the associated Pfam identifiers.

### Details

Each entrez gene identifier maps to a named vector of Pfam identifiers. The name for each Pfam identifier is the IPI accession numbe where this Pfam identifier is found.

If the Pfam is a named NA, it means that the associated Entrez Gene id of this entrez gene identifier is found in an IPI entry of the IPI database, but there is no Pfam identifier in the entry.

If the Pfam is a non-named NA, it means that the associated Entrez Gene id of this entrez gene identifier is not found in any IPI entry of the IPI database.

Mappings were based on data provided by: Yeast Genome ( ftp://genome-ftp.stanford.edu/pub/yeast/data_download ) on 2008-Sep06

### References

Kersey P. J., Duarte J., Williams A., Karavidopoulou Y., Birney E., Apweiler R. The International Protein Index: An integrated database for proteomics experiments. Proteomics 4(7): 1985-1988 (2004) http://www.ebi.ac.uk/IPI/IPIhelp.html

### Examples

            x <- org.Sc.sgdPFAM
            # Get the entrez gene identifiers that are mapped to any Pfam ID
            mapped_genes <- mappedkeys(x)
            # Convert to a list
            xx <- as.list(x[mapped_genes])
            # randomly display 10 genes
            sample(xx, 10)

[Package org.Sc.sgd.db version 2.2.6 Index]