org.Hs.egMAP {org.Hs.eg.db}R Documentation

Map between Entrez Gene Identifiers and cytogenetic maps/bands

Description

org.Hs.egMAP is an R object that provides mappings between entrez gene identifiers and cytoband locations.

Details

Each entrez gene identifier is mapped to a vector of cytoband locations. The vector length may be one or longer, if there are multiple reported chromosomal locations for a given gene. An NA is reported for any entrez gene identifiers that cannot be mapped to a cytoband at this time.

Cytogenetic bands for most higher organisms are labeled p1, p2, p3, q1, q2, q3 (p and q are the p and q arms), etc., counting from the centromere out toward the telomeres. At higher resolutions, sub-bands can be seen within the bands. The sub-bands are also numbered from the centromere out toward the telomere. Thus, a label of 7q31.2 indicates that the band is on chromosome 7, q arm, band 3, sub-band 1, and sub-sub-band 2.

The physical location of each band on a chromosome can be obtained from another object named "organism"CYTOLOC in a separate data package for human(humanCHRLOC), mouse(mouseCHRLOC), and rat(ratCHRLOC).

Mappings were based on data provided by: Entrez Gene ( ftp://ftp.ncbi.nlm.nih.gov/gene/DATA ) on 2008-Apr2

References

http://www.ncbi.nlm.nih.gov

Examples

        x <- org.Hs.egMAP
        # Get the entrez gene identifiers that are mapped to any cytoband
        mapped_genes <- mappedkeys(x)
        # Convert to a list
        xx <- as.list(x[mapped_genes])
        if(length(xx) > 0) {
          # Get the ids for the first five genes
          xx[1:5]
          # Get the first one
          xx[[1]]
        }
        #For the reverse map org.Hs.egMAP2EG
        x <- org.Hs.egMAP2EG
        # Get the cytobands that are mapped to any entrez gene id
        mapped_bands <- mappedkeys(x)
        # Convert to a list
        xx <- as.list(x[mapped_bands])
        if(length(xx) > 0) {
          # Get the bands for the first five genes
          xx[1:5]
          # Get the first one
          xx[[1]]
        }

[Package org.Hs.eg.db version 2.2.0 Index]