agACCNUM {ag.db} | R Documentation

## Map between manufacturer IDs and AGI locus IDs

### Description

`agACCNUM` is an R object that provide mappings between manufacturer IDs and AGI locus IDs.

### Details

Each manufacturer ID is mapped to a vector of AGI locus IDs.

If a manufacturer ID is mapped to multiple AGI locus IDs, then all of these AGI locus IDs will be listed.

For `agACCNUM` an `NA` is assigned to those manufacturer IDs that can not be mapped to an AGI locus ID at this time.

Mappings were based on data provided by: Tair ( ftp://ftp.arabidopsis.org/Microarrays/Affymetrix/affy_AG_array_elements-2008-5-29.txt ) on 2008-Aug12

### See Also

`nhit`

### Examples

      x <- agACCNUM
      # Get the probe identifiers that are mapped to a chromosome
      mapped_probes <- mappedkeys(x)
      # Convert to a list
      xx <- as.list(x[mapped_probes])
      if(length(xx) > 0) {
        # Get the AGI locus IDs for the first five probes
        xx[1:5]
        # Get the first one
        xx[[1]]
      }

    ##   y <- agMULTIHIT
    ##  identical(keys(x), keys(y))    # TRUE

    #  nhx <- nhit(x)
    #  nhy <- nhit(y)
    #  identical(names(nhx), keys(x)) # TRUE
    #  identical(names(nhy), keys(y)) # TRUE
    #  table(nhx)
    #  table(nhy)
    #  onehit_probes <- names(nhx)[nhx != 0 & nhy == 0]
    #  x[[onehit_probes[1]]]          # a single AGI locus ID
    #  y[[onehit_probes[1]]]          # NA
    #  multihit_probes <- names(nhx)[nhy != 0]
    #  x[[multihit_probes[1]]]        # "multiple"
    #  y[[multihit_probes[1]]]        # several AGI locus IDs
    #  nohit_probes <- names(nhx)[nhx == 0]
    #  x[[nohit_probes[1]]]           # NA
    #  y[[nohit_probes[1]]]           # NA
    #  any(nhx == 0 & nhy != 0)       # FALSE
    #  ## Back to a more "normal" map (that combines the data from 'x' and 'y')
    #  xy <- as(x, "AnnDbBimap")      # 'as(y, "AnnDbBimap")' works too
    #  xy[[onehit_probes[1]]]         # a single AGI locus ID
    #  xy[[multihit_probes[1]]]       # several AGI locus IDs
    #  xy[[nohit_probes[1]]]          # NA

[Package ag.db version 2.2.7 Index]