[BioC] Bimap Subsetting

[Hervé Pagès]

Hi Dario,

org.Hs.egSYMBOL is a "direct" map, i.e. it maps from left
to right. This means that keys() is equivalent to Lkeys()
(the "keys" are actually the "left keys").

Subsetting a Bimap by a given set of keys only reduces its
set of "keys" ("left keys" if a direct map, "right keys"
otherwise). In the case of a "direct" map, it means that
the resulting map is now mapping the reduced set of "left keys"
to the original set of "right keys". The set of "right keys"
remains untouched but the number of right keys that are
actually mapped to something on the left is of course smaller:

   > Rlength(org.Hs.egSYMBOL)
   [1] 43051
   > count.mappedRkeys(org.Hs.egSYMBOL)
   [1] 43051

   > Rlength(org.Hs.egSYMBOL[mykeys])
   [1] 43051
   > count.mappedRkeys(org.Hs.egSYMBOL[mykeys])
   [1] 6

If you want to reduce both, the set of left keys and the set
of right keys, consider using subset(). See ?`subset,Bimap-method`
for the details.

Hope this helps,
H.


On 10/21/2012 11:00 PM, Dario Strbenac wrote:
> Hi,
>
> Why does Rkeys gives all of the gene symbols, not just the first 6 ?
>
>> head(names(geneTranscripts)) # Entrez IDs.
> [1] "1"         "10"        "100"       "1000"      "10000"     "100008586"
>
>> length(org.Hs.egSYMBOL[head(names(geneTranscripts))])
> [1] 6
>
>> length(Rkeys(org.Hs.egSYMBOL[head(names(geneTranscripts))]))
> [1] 42075
>
> GenomicFeatures_1.10.0    AnnotationDbi_1.20.2
>
> --------------------------------------
> Dario Strbenac
> PhD Student
> University of Sydney
> Camperdown NSW 2050
> Australia
>
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-- 
Hervé Pagès

Program in Computational Biology
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