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-Oct04

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 2.2.0 Index]