agACCNUM {ag.db} | R Documentation

## Map between manufacturer IDs and AGI locus IDs

### Description

`agACCNUM` and `agMULTIHIT` are R objects that provide mappings between manufacturer IDs and AGI locus IDs.

### Details

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

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

In addition, for `agACCNUM`, the character string `"multiple"` is assigned to those manufacturer IDs that are mapped to more than one AGI locus ID. And for `agMULTIHIT`, an `NA` is also assigned to those manufacturer IDs that are mapped to a single AGI locus ID.

Mappings were based on data provided by: Tair ( ftp://ftp.arabidopsis.org/Microarrays/Affymetrix/affy_AG_array_elements-2007-5-2.txt ) on 2007-Aug2

### See Also

`nhit`

### Examples

      x <- agACCNUM
      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 2.0.2 Index]