I am using getGeneId() in cummeRbund to access geneIds corresponding to TSS ids. I took the following list tssIds as list of TSS identifiers. The order in which getGeneId reports the output is not correct. I then used a loop (slow process) to do the same. I then verified the output by looking into the tss_group_exp.diff file in diff_out file created by cuffdiff program. Somehow this function finds the correct geneID for one tss. The help function does says the following: "A helper function to retrieve the gene_ids for a given list of feature ids (e.g. isoform_ids, tss_group_ids, or CDS_ids). This should not be called directly by the user"

Is this a bug or I am wrong somewhere?

> tssIds
 [1] "TSS10012" "TSS13509" "TSS15074" "TSS16244" "TSS20246" "TSS21819" "TSS21832" "TSS22853" "TSS2357"  "TSS25205" "TSS25461" "TSS25850"
[13] "TSS2743"  "TSS27596" "TSS27750" "TSS29020" "TSS29381" "TSS29959" "TSS33106" "TSS34865" "TSS34874" "TSS37798" "TSS41482" "TSS41653"
[25] "TSS44261" "TSS44669" "TSS45537" "TSS583"   "TSS7773" 
> getGeneId(cuff_data,tssIds)
 [1] "XLOC_000393" "XLOC_001698" "XLOC_002084" "XLOC_005664" "XLOC_007493" "XLOC_010215" "XLOC_011372" "XLOC_012287" "XLOC_015288"
[10] "XLOC_016473" "XLOC_016486" "XLOC_017241" "XLOC_018960" "XLOC_019216" "XLOC_019589" "XLOC_020811" "XLOC_020965" "XLOC_021941"
[19] "XLOC_022194" "XLOC_022598" "XLOC_024932" "XLOC_026302" "XLOC_026306" "XLOC_028613" "XLOC_031368" "XLOC_031539" "XLOC_033562"
[28] "XLOC_033919" "XLOC_034584"
> gids=c(); for(i in 1: length(tssIds)) {gids = c(gids, (getGeneId(cuff_data, tssIds[i])))}
> gids
 [1] "XLOC_007493" "XLOC_010215" "XLOC_011372" "XLOC_012287" "XLOC_015288" "XLOC_016473" "XLOC_016486" "XLOC_017241" "XLOC_001698"
[10] "XLOC_018960" "XLOC_019216" "XLOC_019589" "XLOC_002084" "XLOC_020811" "XLOC_020965" "XLOC_021941" "XLOC_022194" "XLOC_022598"
[19] "XLOC_024932" "XLOC_026302" "XLOC_026306" "XLOC_028613" "XLOC_031368" "XLOC_031539" "XLOC_033562" "XLOC_033919" "XLOC_034584"
[28] "XLOC_000393" "XLOC_005664"