org.Pf.plasmoSYMBOL {org.Pf.plasmo.db}R Documentation

Map between ORF Identifiers and Gene Symbols

Description

org.Pf.plasmoSYMBOL is an R object that provides mappings between ORF identifiers and gene abbreviations.

Details

Each ORF identifier is mapped to the a common abbreviation for the corresponding gene. An NA is reported if there is no known abbreviation for a given gene.

Symbols typically consist of 3 letters that define either a single gene (ABC) or multiple genes (ABC1, ABC2, ABC3). Gene symbols can be used as key words to query public databases such as ORF.

Mappings were based on data provided by: Plasmo DB ( http://plasmodb.org/common/downloads/release-5.4/Pfalciparum ) on 31-Oct-2007

References

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene

Examples

        x <- org.Pf.plasmoSYMBOL
        # Get the gene symbol that are mapped to an ORF identifiers
        mapped_genes <- mappedkeys(x)
        # Convert to a list
        xx <- as.list(x[mapped_genes])
        if(length(xx) > 0) {
          # Get the SYMBOL for the first five genes
          xx[1:5]
          # Get the first one
          xx[[1]]
        }
        # For the reverse map:
        x <- org.Pf.plasmoSYMBOL2ORF
        # Get the ORF identifiers that are mapped to a gene symbol
        mapped_genes <- mappedkeys(x)
        # Convert to a list
        xx <- as.list(x[mapped_genes])
        if(length(xx) > 0) {
          # Get the ORF ID for the first five genes
          xx[1:5]
          # Get the first one
          xx[[1]]
        }

[Package org.Pf.plasmo.db version 2.2.0 Index]