agACCNUM {ag.db} | R Documentation |
agACCNUM
and agMULTIHIT
are R objects
that provide mappings between manufacturer IDs and AGI locus IDs.
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
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