On 10/22/2012 09:48 AM, Hervé Pagès wrote: > 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 > FWIW, an analogy can be made with subsetting a factor where, by default, the unused levels are not dropped: > x <- factor(letters[1:10]) > x [1] a b c d e f g h i j Levels: a b c d e f g h i j > x[1:6] [1] a b c d e f Levels: a b c d e f g h i j unless you use drop=TRUE: > x[1:6, drop=TRUE] [1] a b c d e f Levels: a b c d e f So we could support a similar feature on Bimap objects thru the 'drop' argument, which is ignored at the moment: > Rlength(org.Hs.egSYMBOL[mykeys, drop=FALSE]) [1] 43051 > Rlength(org.Hs.egSYMBOL[mykeys, drop=TRUE]) [1] 43051 However, an easy way to drop unused (i.e. unmapped) keys is: Lkeys(x) <- mappedLkeys(x) # drop unused left keys Rkeys(x) <- mappedRkeys(x) # drop unused right keys or (as mentioned earlier): subset(x, Lkeys=mappedLkeys(x), Rkeys=mappedRkeys(x)) Cheers, H. > 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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319