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