Dear Valerie, thank you SO much for giving me hope that I will recover this structure. But I still couldn't figure out how to do it. I'm still with R 3.2.
#today, Dec 09 2016
> biocValid()
* sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04 LTS
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] BiocInstaller_1.20.3 AnnotationHub_2.2.5 BSgenome_1.38.0
[4] rtracklayer_1.30.4 Biostrings_2.38.4 XVector_0.10.0
[7] GenomicRanges_1.22.4 GenomeInfoDb_1.6.3 IRanges_2.4.8
[10] S4Vectors_0.8.11 BiocGenerics_0.16.1 RSQLite_1.0.0
[13] DBI_0.5-1
update with biocLite()
Error: 20 package(s) out of date
I tried to do the following :
> hub = AnnotationHub()
snapshotDate(): 2016-12-08
> possibleDates(hub)
# I got a list of 63 dates
>snapshotDate(hub) = "2016-07-20"
# I tried a few other dates, but I think that should be the right one
> query(hub, "communis")
AnnotationHub with 1 record
# snapshotDate(): 2016-07-20
# names(): AH10581
# $dataprovider: Inparanoid8
# $species: Ricinus communis
#That's the other only available thing on Ricinus communis, and it's not the one I want (AH48041 is the right one). There were 2 records originally, the other one was the OrgDb.
So I could not set AnnotationHub to a different date, and I still have the old versions of R/Bioconductor tha I hoped would make the trick. Please help me!!!
A comment: if you work with humans and have daily updates on data that is all very good, but this structure is the only one available with the correlation ENTREZID, Symbol, GO that I found anywhere for this species. Not nice when it's not available... Thank you in advance, Ana.
Just fyi, when you respond to an answer or comment use 'ADD COMMENT' instead of posting a new answer.
I am able to get this resource with R-3-2 and snapshot date of "2016-07-20".
> library(AnnotationHub)
> hub <- AnnotationHub()
snapshotDate(): 2016-12-08
Change the date:
> snapshotDate(hub) <- "2016-07-20"
> hub
AnnotationHub with 36164 records
# snapshotDate(): 2016-07-20
# $dataprovider: BroadInstitute, UCSC, Ensembl, ftp://ftp.ncbi.nlm.nih.gov/g...
# $species: Homo sapiens, Mus musculus, Bos taurus, Pan troglodytes, Danio r...
# $rdataclass: GRanges, BigWigFile, FaFile, ChainFile, OrgDb, TwoBitFile, In...
# additional mcols(): taxonomyid, genome, description, tags, sourceurl,
...
Extract AH48041:
> hub["AH48041"]
AnnotationHub with 1 record
# snapshotDate(): 2016-07-20
# names(): AH48041
# $dataprovider: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Ricinus communis
# $rdataclass: OrgDb
# $title: org.Ricinus_communis.eg.sqlite
# $description: NCBI gene ID based annotations about Ricinus_communis
# $taxonomyid: 3988
# $genome: NCBI genomes
# $sourcetype: NCBI/UniProt
# $sourceurl: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/, ftp://ftp.uniprot.org/p...
# $sourcelastmodifieddate: NA
# $sourcesize: NA
# $tags: NCBI, Gene, Annotation
# retrieve record with 'object[["AH48041"]]'
> sessionInfo()
R version 3.2.5 Patched (2016-05-05 r71773)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Fedora 24 (Workstation Edition)
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 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] AnnotationHub_2.2.5 BiocGenerics_0.16.1
loaded via a namespace (and not attached):
[1] Rcpp_0.12.8 IRanges_2.4.8
[3] digest_0.6.10 mime_0.5
[5] R6_2.2.0 xtable_1.8-2
[7] DBI_0.5-1 stats4_3.2.5
[9] RSQLite_1.1-1 BiocInstaller_1.20.3
[11] httr_1.2.1 curl_2.3
[13] S4Vectors_0.8.11 Biobase_2.30.0
[15] shiny_0.14.2 httpuv_1.3.3
[17] AnnotationDbi_1.32.3 memoise_1.0.0
[19] htmltools_0.3.5 interactiveDisplayBase_1.8.0
Thank you so much Valerie, I managed to find the object after all after changing the snapshot date:
> library(AnnotationHub)
>ah = AnnotationHub()
>snapshotDate(ah) = "2016-07-20"
>ah["AH48041"]
>obj = ah[["AH48041"]]
OK, it worked, problem solved, accolades to you! Ana