[Bioc-devel] Converting gene ids to GRanges - ensembl centric TxDb missing for human

[Bhagwat, Aditya]

Thankyou Lori,

Cheers,

Aditya


________________________________
From: Shepherd, Lori [Lori.Shepherd using RoswellPark.org]
Sent: Tuesday, October 15, 2019 2:22 PM
To: Bhagwat, Aditya; bioc-devel using r-project.org
Subject: Re: Converting gene ids to GRanges - ensembl centric TxDb missing for human

Again we would not recommend posting these types of questions to both the mailing list and the support site.
Since this is not a developer question -  the support site was the appropriate place -
https://support.bioconductor.org/p/125609/

We have members of the team working on developing the new TxDbs for the release and will look into the reasoning and post on the support site thread.



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Bhagwat, Aditya <Aditya.Bhagwat using mpi-bn.mpg.de>
Sent: Tuesday, October 15, 2019 8:15 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Converting gene ids to GRanges - ensembl centric TxDb missing for human

Dear BioC devel,

I want to convert geneids to GRanges by doing:
        GenomicFeatures::genes(txdb)[geneids]

Works wonderfully for mouse, with entrezgene as well ensemblgene-centric TxDbs:
        txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene::TxDb.Mmusculus.UCSC.mm10.knownGene
        GenomicFeatures::genes(txdb)[c('100009600', '99889', '99982')]

        txdb <- TxDb.Mmusculus.UCSC.mm10.ensGene::TxDb.Mmusculus.UCSC.mm10.ensGene
        GenomicFeatures::genes(txdb)[c('ENSMUSG00000000001', 'ENSMUSG00000000003')]

For human, hower, ensembl-centric TxDbs seem to be missing:
        txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene::TxDb.Hsapiens.UCSC.hg38.knownGene
        GenomicFeatures::genes(txdb)[c('1', '10', '100')]

       # No TxDb.Hsapiens.UCSC.hg38.ensGene::TxDb.Hsapiens.UCSC.hg38.ensGene

Has this been a (perhaps recent) design choice to no longer offer the ensemble-centric TxDbs?

(The larger context of this question is the development of multicrispr (https://gitlab.gwdg.de/loosolab/software/multicrispr))

Thankyou for feedback!

Aditya

        [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel using r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.

	[[alternative HTML version deleted]]