[BioC] Rkeys function from AnnotationDbi returns all Rkeys for a subset

[Leon Yee]

Dear all,

     I encountered a problem when I using Rkeys from AnnotationDbi
package. Using [] I get a subset of a AnnDbBimap object, but when I
using Rkeys for this subset, it returns all of the Rkeys from the
original set.

> library("hgu95av2.db")
> ids = ls(hgu95av2PATH)
> as.list(hgu95av2PATH[ids[1:5]])
$`1000_at`
 [1] "04010" "04012" "04150" "04350" "04360" "04370" "04510" "04520" "04540"
[10] "04620" "04650" "04664" "04720" "04730" "04810" "04910" "04912" "04916"
[19] "04930" "05210" "05211" "05212" "05213" "05214" "05215" "05216" "05218"
[28] "05219" "05220" "05221" "05223"

$`1001_at`
[1] NA

$`1002_f_at`
[1] "00590" "00591" "00830" "00902" "00903" "00980" "00982"

$`1003_s_at`
[1] "04060"

$`1004_at`
[1] "04060"

> Rkeys(hgu95av2PATH[ids[1:5]])
# this is expected to output only the  PATH ids as outputed of the
# previous command, but it outputed all the PATH ids.

  [1] "00010" "00020" "00030" "00031" "00040" "00051" "00052" "00053"
"00061"
 [10] "00062" "00071" "00072" "00100" "00120" "00130" "00140" "00150"
"00190"
 [19] "00220" "00230" "00232" "00240" "00251" "00252" "00260" "00271"
"00272"
 [28] "00280" "00281" "00290" "00300" "00310" "00330" "00340" "00350"
"00360"
 [37] "00361" "00363" "00380" "00400" "00401" "00410" "00430" "00440"
"00450"
 [46] "00460" "00471" "00472" "00480" "00500" "00510" "00511" "00512"
"00520"
 [55] "00521" "00530" "00531" "00532" "00533" "00534" "00550" "00561"
"00562"
 [64] "00563" "00564" "00565" "00590" "00591" "00592" "00600" "00601"
"00602"
 [73] "00603" "00604" "00620" "00624" "00625" "00630" "00632" "00640"
"00641"
 [82] "00643" "00650" "00660" "00670" "00680" "00710" "00720" "00730"
"00740"
 [91] "00750" "00760" "00770" "00780" "00785" "00790" "00791" "00830"
"00860"
[100] "00900" "00902" "00903" "00910" "00920" "00930" "00940" "00950"
"00960"
[109] "00970" "00980" "00982" "00983" "01030" "01031" "01032" "01040"
"01430"
[118] "01510" "02010" "03010" "03020" "03022" "03030" "03050" "03060"
"03320"
[127] "03410" "03420" "03430" "03440" "03450" "04010" "04012" "04020"
"04060"
[136] "04070" "04080" "04110" "04115" "04120" "04130" "04140" "04150"
"04210"
[145] "04310" "04330" "04340" "04350" "04360" "04370" "04510" "04512"
"04514"
[154] "04520" "04530" "04540" "04610" "04612" "04614" "04620" "04630"
"04640"
[163] "04650" "04660" "04662" "04664" "04670" "04710" "04720" "04730"
"04740"
[172] "04742" "04810" "04910" "04912" "04916" "04920" "04930" "04940"
"04950"
[181] "05010" "05020" "05030" "05040" "05050" "05060" "05110" "05120"
"05130"
[190] "05131" "05210" "05211" "05212" "05213" "05214" "05215" "05216"
"05217"
[199] "05218" "05219" "05220" "05221" "05222" "05223" "05310" "05320"
"05322"
[208] "05330" "05332" "05340"

> sessionInfo()
R version 2.8.0 (2008-10-20)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=C;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] hgu95av2.db_2.2.5   RSQLite_0.7-1       DBI_0.2-4
[4] AnnotationDbi_1.4.1 Biobase_2.2.1


  Can anybody help? Thanks a lot!

Leon