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
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