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Question: Why does Homo.sapiens import TxDb.Hsapiens.UCSC.hg19.knownGene instead of TxDb.Hsapiens.UCSC.hg38.knownGene?
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gravatar for enricoferrero
19 months ago by
enricoferrero550
United Kingdom
enricoferrero550 wrote:

 Why does Homo.sapiens import TxDb.Hsapiens.UCSC.hg19.knownGene instead of TxDb.Hsapiens.UCSC.hg38.knownGene?

> library(Homo.sapiens)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GO.db
Loading required package: DBI
Loading required package: org.Hs.eg.db
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now getting the TxDb Object directly

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.7 (Santiago)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=C               LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=C              LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] Homo.sapiens_1.3.1                      TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 org.Hs.eg.db_3.2.3                      GO.db_3.2.2                             RSQLite_1.0.0                           DBI_0.3.1
 [7] OrganismDbi_1.12.1                      GenomicFeatures_1.22.13                 GenomicRanges_1.22.4                    GenomeInfoDb_1.6.3                      AnnotationDbi_1.32.3                    IRanges_2.4.8
[13] S4Vectors_0.8.11                        Biobase_2.30.0                          BiocGenerics_0.16.1                     BiocInstaller_1.20.1                    vimcom_1.2-7.2                          colorout_1.0-2
[19] setwidth_1.0-4

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.3                futile.logger_1.4.1        XVector_0.10.0             bitops_1.0-6               futile.options_1.0.0       tools_3.2.2                zlibbioc_1.16.0            biomaRt_2.26.1             graph_1.48.0               Rgraphviz_2.14.0
[11] rtracklayer_1.30.3         CellNOptR_1.16.0           Biostrings_2.38.4          grid_3.2.2                 XML_3.98-1.4               RBGL_1.46.0                BiocParallel_1.4.3         lambda.r_1.1.7             Rsamtools_1.22.0           GenomicAlignments_1.6.3
[21] SummarizedExperiment_1.0.2 colorspace_1.2-6           RCurl_1.95-4.8

Thank you,

ADD COMMENTlink modified 19 months ago by Valerie Obenchain ♦♦ 6.4k • written 19 months ago by enricoferrero550
1
gravatar for Valerie Obenchain
19 months ago by
Valerie Obenchain ♦♦ 6.4k
United States
Valerie Obenchain ♦♦ 6.4k wrote:

Hi,

The OrganismDb packages are fairly new and currently we only have 3 pre-built packages for human, rat and mouse. This first round we chose a general naming convention vs the more descriptive one used for BSgenome or TxDb. We plan to continue development on this class after the April release, see this discussion. Please add your 2 cents there - the more feedback the better.

You can make your own OrganismDb with a different TxDb using one of these helpers:

library(OrganismDbi)

> ?makeOrganism <hit tab>
?makeOrganismDbFromBiomart  ?makeOrganismDbFromTxDb     ?makeOrganismDbFromUCSC     ?makeOrganismPackage

Valerie

ADD COMMENTlink written 19 months ago by Valerie Obenchain ♦♦ 6.4k
3

Also note that you can use the TxDb accessor to change the TxDb that you are using

> library(Homo.sapiens)
> library(TxDb.Hsapiens.UCSC.hg38.knownGene)
> TxDb(Homo.sapiens) <- TxDb.Hsapiens.UCSC.hg38.knownGene
Now getting the GODb Object directly
Now getting the OrgDb Object directly
Now loading the TxDb Object from local disc
> Homo.sapiens
OrganismDb Object:
# Includes GODb Object:  GO.db
# With data about:  Gene Ontology
# Includes OrgDb Object:  org.Hs.eg.db
# Gene data about:  Homo sapiens
# Taxonomy Id:  9606
# Includes TxDb Object:  TxDb.Hsapiens.UCSC.hg38.knownGene
# Transcriptome data about:  Homo sapiens
# Based on genome:  hg38
# The OrgDb gene id ENTREZID is mapped to the TxDb gene id GENEID .

Which is sort of a pain, but in the end is only two extra lines of code.

ADD REPLYlink modified 19 months ago • written 19 months ago by James W. MacDonald45k

Nice, thanks!

ADD REPLYlink written 19 months ago by enricoferrero550

Thanks Valerie,

I just have one comment: since the OrganismDb packages do not refer to a specific genome build with their names, I would expect them to use the current one (i.e.: GRCh38). I don't see any reason to use GRCh37/hg19 these days.

Cheers,

ADD REPLYlink written 19 months ago by enricoferrero550
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