agCHR {ag}R Documentation

Map Manufacturer IDs to Chromosomes

Description

agCHR is an R environment that provides mappings between a manufacturer identifier and the chromosome that contains the gene of interest.

Details

Each manufacturer identifier maps to a vector of chromosomes. Due to inconsistencies that may exist at the time the environment was built, the vector may contain more than one chromosome (e.g., the identifier may map to more than one chromosome). If the chromosomal location is unknown, the vector will contain an NA.

Mappings were based on data provided by:

Tair: ftp://ftp.arabidopsis.org/home/tair/Microarrays/Affymetrix/affy_AG_array_elements-2006-07-14.txt Tair: ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR_sequenced_genes Tair: ftp://ftp.arabidopsis.org/home/tair/User_Requests/LocusPublished.02022007 Built: N/A

Package built: Fri Aug 24 17:42:16 2007

Examples

        # Convert to a list
        xx <- as.list(agCHR)
        # Remove probe identifiers that do not map to any CHRLOC
        xx <- xx[!is.na(xx)]
        if(length(xx) > 0){
            # Get the chromosome number for the first five probes
            xx[1:5]
            # Get the first one
            xx[[1]]
        }

[Package ag version 2.2.0 Index]