As well as
> subsetByOverlaps(transcripts(Homo.sapiens), GRanges("chrM:1-16569"))
'select()' returned 1:1 mapping between keys and columns
GRanges object with 37 ranges and 2 metadata columns:
seqnames ranges strand | TXID TXNAME
<Rle> <IRanges> <Rle> | <IntegerList> <CharacterList>
[1] chrM 577-647 + | 252799 ENST00000387314.1
[2] chrM 648-1601 + | 252800 ENST00000389680.2
[3] chrM 1602-1670 + | 252801 ENST00000387342.1
[4] chrM 1671-3229 + | 252802 ENST00000387347.2
[5] chrM 3230-3304 + | 252803 ENST00000386347.1
... ... ... ... . ... ...
[33] chrM 5826-5891 - | 252831 ENST00000387409.1
[34] chrM 7446-7514 - | 252832 ENST00000387416.2
[35] chrM 14149-14673 - | 252833 ENST00000361681.2
[36] chrM 14674-14742 - | 252834 ENST00000387459.1
[37] chrM 15956-16023 - | 252835 ENST00000387461.2
-------
seqinfo: 711 sequences (1 circular) from hg38 genome
However
> subsetByOverlaps(transcriptsBy(Homo.sapiens), GRanges("chrM:1-16569"))
GRangesList object of length 0:
<0 elements>
And
> subsetByOverlaps(transcripts(Homo.sapiens, columns = c("GENEID","SYMBOL")),
> GRanges("chrM:1-16569"))
'select()' returned 1:1 mapping between keys and columns
GRanges object with 37 ranges and 2 metadata columns:
seqnames ranges strand | GENEID SYMBOL
<Rle> <IRanges> <Rle> | <CharacterList> <CharacterList>
[1] chrM 577-647 + | <NA> <NA>
[2] chrM 648-1601 + | <NA> <NA>
[3] chrM 1602-1670 + | <NA> <NA>
[4] chrM 1671-3229 + | <NA> <NA>
[5] chrM 3230-3304 + | <NA> <NA>
... ... ... ... . ... ...
[33] chrM 5826-5891 - | <NA> <NA>
[34] chrM 7446-7514 - | <NA> <NA>
[35] chrM 14149-14673 - | <NA> <NA>
[36] chrM 14674-14742 - | <NA> <NA>
[37] chrM 15956-16023 - | <NA> <NA>
-------
seqinfo: 711 sequences (1 circular) from hg38 genome
Everything is mapped via the GENEID, and if you query the UCSC genome browser
for hg38/knownGene, asking for gene name, known gene ID and gene symbol, you
will get the first and last but not the middle.
-----Original Message-----
From: Bioc-devel <bioc-devel-boun...@r-project.org> On Behalf Of Vincent Carey
Sent: Thursday, March 28, 2024 10:00 AM
To: Tim Triche, Jr. <tim.tri...@gmail.com>
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Bioconductor 3.19 db0s, OrgDbs, and TxDbs now
available
winging it here tim
> select(Homo.sapiens, keys="ENSG00000198727", keytype="ENSEMBL",
columns=c("GENENAME", "GENEID", "CDSCHROM", "SYMBOL")) 'select()' returned 1:1
mapping between keys and columns
ENSEMBL GENENAME SYMBOL CDSCHROM GENEID
1 ENSG00000198727 cytochrome b CYTB <NA> 4519
> select(Homo.sapiens, keys= "MTCYBP1", keytype="SYMBOL",
columns=c("GENENAME", "GENEID", "CDSCHROM", "SYMBOL")) 'select()' returned 1:1
mapping between keys and columns
SYMBOL GENENAME CDSCHROM GENEID
1 MTCYBP1 MT-CYB pseudogene 1 <NA> 100499418
relevant?
On Thu, Mar 28, 2024 at 9:17 AM Tim Triche, Jr. <tim.tri...@gmail.com>
wrote:
> Hi Lori and fellow maintainers,
>
> I had a strange experience yesterday where I pulled down genes and
> transcripts from Homo.sapiens, only to discover that all mitochondrial
> encoded genes (MT-CYB, MT-CO2, etc) were missing.
>
> Is there an historical reason why this is so? Obviously these
> transcripts are physiologically important, but beyond that, they’re
> also used all the time in single cell sequencing to estimate viability.
>
> Best,
>
> --t
>
> > On Mar 28, 2024, at 8:47 AM, Kern, Lori via Bioc-devel <
> bioc-devel@r-project.org> wrote:
> >
> > Hello Bioconductor community,
> >
> > The newest db0, OrgDb, and TxDb annotation packages for the upcoming
> Bioconductor 3.19 release are up and available for download in the
> devel version of Bioconductor.
> >
> > The deadline for submitting contributed annotation packages will be
> Wednesday April 17 th.
> >
> > The new db0 packages are:
> >
> > anopheles.db0_3.19.0.tar.gz
> > arabidopsis.db0_3.19.0.tar.gz
> > bovine.db0_3.19.0.tar.gz
> > canine.db0_3.19.0.tar.gz
> > chicken.db0_3.19.0.tar.gz
> > chimp.db0_3.19.0.tar.gz
> > ecoliK12.db0_3.19.0.tar.gz
> > ecoliSakai.db0_3.19.0.tar.gz
> > fly.db0_3.19.0.tar.gz
> > human.db0_3.19.0.tar.gz
> > malaria.db0_3.19.0.tar.gz
> > mouse.db0_3.19.0.tar.gz
> > pig.db0_3.19.0.tar.gz
> > rat.db0_3.19.0.tar.gz
> > rhesus.db0_3.19.0.tar.gz
> > worm.db0_3.19.0.tar.gz
> > xenopus.db0_3.19.0.tar.gz
> > yeast.db0_3.19.0.tar.gz
> > zebrafish.db0_3.19.0.tar.gz
> >
> > The new OrgDb packages are:
> >
> > GO.db_3.19.0.tar.gz
> > org.Ag.eg.db_3.19.0.tar.gz
> > org.At.tair.db_3.19.0.tar.gz
> > org.Bt.eg.db_3.19.0.tar.gz
> > org.Ce.eg.db_3.19.0.tar.gz
> > org.Cf.eg.db_3.19.0.tar.gz
> > org.Dm.eg.db_3.19.0.tar.gz
> > org.Dr.eg.db_3.19.0.tar.gz
> > org.EcK12.eg.db_3.19.0.tar.gz
> > org.EcSakai.eg.db_3.19.0.tar.gz
> > org.Gg.eg.db_3.19.0.tar.gz
> > org.Hs.eg.db_3.19.0.tar.gz
> > org.Mm.eg.db_3.19.0.tar.gz
> > org.Mmu.eg.db_3.19.0.tar.gz
> > org.Pt.eg.db_3.19.0.tar.gz
> > org.Rn.eg.db_3.19.0.tar.gz
> > org.Sc.eg.db_3.19.0.tar.gz
> > org.Ss.eg.db_3.19.0.tar.gz
> > org.Xl.eg.db_3.19.0.tar.gz
> > Orthology.eg.db_3.19.0.tar.gz
> > PFAM.db_3.19.0.tar.gz
> >
> > The new TxDb packages are:
> >
> > TxDb.Hsapiens.UCSC.hg38.refGene_3.19.0.tar.gz
> > TxDb.Mmusculus.UCSC.mm39.refGene_3.19.0.tar.gz
> >
> > Thank you
> >
> >
> > Lori Shepherd - Kern
> >
> > Bioconductor Core Team
> >
> > Roswell Park Comprehensive Cancer Center
> >
> > Department of Biostatistics & Bioinformatics
> >
> > Elm & Carlton Streets
> >
> > Buffalo, New York 14263
> >
> >
> > This email message may contain legally privileged and/or
> > confidential
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> >
> > _______________________________________________
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