org.At.tairCHRLOC {org.At.tair.db}R Documentation

Map Manufacturer IDs to Chromosomal Location

Description

org.At.tairCHRLOC is an R object that maps manufacturer identifiers to the starting position of the gene. The position of a gene is measured as the number of base pairs.

The CHRLOCEND mapping is the same as the CHRLOC mapping except that it specifies the ending base of a gene instead of the start.

Details

Each manufacturer identifier maps to a named vector of chromosomal locations, where the name indicates the chromosome. Due to inconsistencies that may exist at the time the object was built, these vectors may contain more than one chromosome and/or location. If the chromosomal location is unknown, the vector will contain an NA.

Chromosomal locations on both the sense and antisense strands are measured as the number of base pairs from the p (5' end of the sense strand) to q (3' end of the sense strand) arms. Chromosomal locations on the antisense strand have a leading "-" sign (e. g. -1234567).

Mappings were based on data provided by: Tair ftp://ftp.arabidopsis.org/Maps/seqviewer\_data/sv\_gene.data With a date stamp from the source of: 2011-May27

Examples

        x <- org.At.tairCHRLOC
        # Get the tair identifiers that are mapped to chromosome locations
        mapped_tairs <- mappedkeys(x)
        # Convert to a list
        xx <- as.list(x[mapped_tairs])
        if(length(xx) > 0) {
          # Get the CHRLOC for the first five tairs
          xx[1:5]
          # Get the first one
          xx[[1]]
        }

[Package org.At.tair.db version 2.6.4 Index]