org.Hs.egMAP {org.Hs.eg.db} | R Documentation |
org.Hs.egMAP is an R object that provides mappings between entrez gene identifiers and cytoband locations.
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
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]] }