I've pushed new 3.8.2 orgdbs that should propagate soon. They do not have this
issue.
________________________________
From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Pages, Herve
<hpa...@fredhutch.org>
Sent: Thursday, April 25, 2019 9:19:35 PM
To: Aaron Lun; Vincent Carey
Cc: Bioc-devel; jmac...@u.washington.edu
Subject: Re: [Bioc-devel] Weird monkey identifiers in org.Hs.eg.db
Hi Aaron,
On 4/25/19 16:44, Aaron Lun wrote:
It doesn't seem like it - on my installation, org.Hs.eg.db is still...
monkeying around.
__
w c(..)o (
\__(-) __)
/\ (
/(_)___)
w /|
| \
m m
Daniel has prepared a new batch of *.db0 and org.* packages (v 3.8.1). The new
packages are on their way and should become available via
BiocManager::install() in the next 12 hours or so.
Hopefully they'll put an end to the Great Monkey Conspiracy!
Unfortunately we won't see the effect on tomorrow's build report, only on
Saturday's report.
Cheers,
H.
On Thu, Apr 25, 2019 at 9:17 AM Vincent Carey
<st...@channing.harvard.edu><mailto:st...@channing.harvard.edu>
wrote:
Has this situation been rectified?
On Tue, Apr 23, 2019 at 11:40 AM Van Twisk, Daniel <
daniel.vantw...@roswellpark.org<mailto:daniel.vantw...@roswellpark.org>> wrote:
We've made some changes to our annotation generation scripts this release
and it seems these may have introduced some errors. Thank you for
identifying this issue and I will try to have some fixes out asap.
________________________________
From: Bioc-devel
<bioc-devel-boun...@r-project.org><mailto:bioc-devel-boun...@r-project.org> on
behalf of James
W. MacDonald <jmac...@uw.edu><mailto:jmac...@uw.edu>
Sent: Tuesday, April 23, 2019 11:03:02 AM
To: Aaron Lun
Cc: Bioc-devel
Subject: Re: [Bioc-devel] Weird monkey identifiers in org.Hs.eg.db
Looks like the ensembl table of the human.db0 package got polluted with
*Pan
troglodytes* genes:
con <- dbConnect(SQLite(),
"/R-devel/lib64/R/library/human.db0/extdata/chipsrc_human.sqlite")
dbGetQuery(con, "select count(*) from ensembl where ensid like
'ENSPTR%';")
count(*)
1 16207
dbGetQuery(con, "select count(*) from ensembl where ensid like
'ENSG%';")
count(*)
1 28973
On Mon, Apr 22, 2019 at 11:54 PM Aaron Lun <
infinite.monkeys.with.keyboa...@gmail.com<mailto:infinite.monkeys.with.keyboa...@gmail.com>>
wrote:
Playing around with org.Hs.eg.db 3.8.0. What on earth is ENSPTRG0000...?
> library(org.Hs.eg.db)
> mapIds(org.Hs.eg.db, key="GCG", keytype="SYMBOL", column="ENSEMBL")
'select()' returned 1:many mapping between keys and columns
GCG
"ENSPTRG00000000777"
Well, at least it still recovers the right identifier... eventually.
> select(org.Hs.eg.db, key="GCG", keytype="SYMBOL", columns="ENSEMBL")
'select()' returned 1:many mapping between keys and columns
SYMBOL ENSEMBL
1 GCG ENSPTRG00000000777
2 GCG ENSG00000115263
The SYMBOL->Entrez ID relational table seems to be okay:
> Y <- toTable(org.Hs.egSYMBOL)
> Y[which(Y[,2]=="GCG"),]
gene_id symbol
2152 2641 GCG
So the cause is the Ensembl->Entrez mappings:
> Z <- toTable(org.Hs.egENSEMBL2EG)
> Z[Z[,1]==2641,]
gene_id ensembl_id
3028 2641 ENSPTRG00000000777
3029 2641 ENSG00000115263
Googling suggests that ENSPTRG00000000777 is an identifier for some
other gene in one of the other monkeys. Hardly "Hs" stuff.
Session info (not technically R 3.6, but I didn't think that would have
been the cause):
R Under development (unstable) (2019-04-11 r76379)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS
Matrix products: default
BLAS: /home/luna/Software/R/trunk/lib/libRblas.so
LAPACK: /home/luna/Software/R/trunk/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils
datasets
[8] methods base
other attached packages:
[1] org.Hs.eg.db_3.8.0 AnnotationDbi_1.45.1 IRanges_2.17.5
[4] S4Vectors_0.21.23 Biobase_2.43.1 BiocGenerics_0.29.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 digest_0.6.18 DBI_1.0.0 RSQLite_2.1.1
[5] blob_1.1.1 bit64_0.9-7 bit_1.1-14 compiler_3.7.0
[9] pkgconfig_2.0.2 memoise_1.1.0
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University of Washington
Environmental and Occupational Health Sciences
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Division of Public Health Sciences
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