chickenPFAM {chicken.db} | R Documentation

## Map Manufacturer IDs to Pfam IDs

### Description

chickenPFAM is an R object that provides mappings between a manufacturer identifier and the associated Pfam identifiers.

### Details

Each manufacturer 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 manufacturer 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 manufacturer identifier is not found in any IPI entry of the IPI database.

Mappings were based on data provided by: The International Protein Index ( ftp://ftp.ebi.ac.uk/pub/databases/IPI/current ) on 2008-Sep02

### 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 <- chickenPFAM
            # Get the probe identifiers that are mapped to any Pfam ID
            mapped_probes <- mappedkeys(x)
            # Convert to a list
            xx <- as.list(x[mapped_probes])
            # randomly display 10 probes
            sample(xx, 10)

[Package chicken.db version 2.2.5 Index]