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11.7 years ago
fm271
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20
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"
Are you using the latest version of cummeRbund? The current version is 2.0. You can find your version using sessionInfo(). This forum is probably not the best place to post bioconductor package related questions, the best place would be their mailing list: http://www.bioconductor.org/help/mailing-list/#bioconductor make sure you follow the posting guidelines