Re: [Bioc-devel] OrganismDb package for Drosophila.melanogaster
On Tue, Nov 15, 2016 at 7:34 PM, Martin Morgan wrote:
> On 11/15/2016 09:52 AM, Obenchain, Valerie wrote:
>> On 11/15/2016 03:32 AM, Pariksheet Nanda wrote:
>>>
>>> It would be great to have an OrganismDb package for
>>> Drosophila.melanogaster, similar to Homo.sapiens, Mus.musculus and
>>> Rattus.norvegicus.
--snip--
>>> In other words, like Rattus.norvegicus, it might be good do add a UCSC
>>> "refGene" TxDb package for dm6 as "ensGene" doesn't appear to be as
good of
>>> a candidate (at least without some ugliness)? I was looking at
creating a
>>> dm6 UCSC "refGene" TxDb.
>>
>> You can use GenomicFeatures::makeTxDbFromUCSC() to create the TxDb. The
>> man page, ?makeTxDbFromUCSC, also has helper functions that display
>> available genomes, tables and tracks.
>
> I'm not completely sure of the result, but
>
> library(OrganismDb)
> odb = makeOrganismDbFromUCSC("dm6", tableName="refGene")
>
> might be most of the way there?
Thanks Valerie and Martin for pointing out the make*() functions!
As my lab uses the same UCSC tables frequently, I used the
make*Package() functions (namely,
GenomicFeatures::makeTxDbPackageFromUCSC and
OrganismDbi::makeOrganismPackage).
For others who run OrganismDbi::makeOrganismPackage, don't forget
to edit the generated PACKAGE file and add your new TxDb package
to "Depends".
>> Valerie
> Martin
Pariksheet
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] OrganismDb package for Drosophila.melanogaster
On 11/15/2016 09:52 AM, Obenchain, Valerie wrote:
Hi Pariksheet,
On 11/15/2016 03:32 AM, Pariksheet Nanda wrote:
Hi folks,
It would be great to have an OrganismDb package for
Drosophila.melanogaster, similar to Homo.sapiens, Mus.musculus and
Rattus.norvegicus.
While trying to do this on my own using the Homo.sapiens package as a
starting point, I found the most similar looking keys to relate
org.Dm.eg.db and TxDb.Dmelanogaster.UCSC.dm6.ensGene to be "ENSEMBL" and
"GENEID" though there's a ".1" tacked to the end "GENEID" which makes it
harder to supply the graphInfo object to OrganismDbi:::.loadOrganismDbiPkg:
!> key_ <- function(db, key) sort(as.character(
+select(db, keys(db, key), key,
key)[[key]]))
> key_head <- function(db, key) head(key_(db, key))
> key_head(TxDb.Dmelanogaster.UCSC.dm6.ensGene, "GENEID")
'select()' returned 1:1 mapping between keys and columns
[1] "FBgn003.1" "FBgn008.1" "FBgn014.1" "FBgn015.1"
[5] "FBgn017.1" "FBgn018.1"
> key_head(org.Dm.eg.db, "ENSEMBL")
[1] "FBgn008" "FBgn014" "FBgn015" "FBgn017" "FBgn018"
[6] "FBgn022"
>
In other words, like Rattus.norvegicus, it might be good do add a UCSC
"refGene" TxDb package for dm6 as "ensGene" doesn't appear to be as good of
a candidate (at least without some ugliness)? I was looking at creating a
dm6 UCSC "refGene" TxDb.
You can use GenomicFeatures::makeTxDbFromUCSC() to create the TxDb. The
man page, ?makeTxDbFromUCSC, also has helper functions that display
available genomes, tables and tracks.
I'm not completely sure of the result, but
library(OrganismDb)
odb = makeOrganismDbFromUCSC("dm6", tableName="refGene")
might be most of the way there?
Martin
Valerie
I imagine one would query the UCSC public MySQL
server and then do the SQLite conversion. Although the conversion to
SQLite seems a bit finagly as the datatypes differ between MySQL and SQLite
and I'm having a hard time finding a well supported tool to do it; I don't
want to introduce errors or harm reproducibility. What do you use for
MySQL to SQLite conversion? Or would it be more sensible for you
benevolent dictators to generate the package(s)?
Pariksheet
---
Pariksheet Nanda
PhD Candidate in Genetics and Genomics
System Administrator, Storrs HPC Cluster
University of Connecticut
---
> sessionInfo()
R Under development (unstable) (2016-11-13 r71655)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_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] stats4parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] Rattus.norvegicus_1.3.1
[2] TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.0
[3] org.Rn.eg.db_3.4.0
[4] Mus.musculus_1.3.1
[5] TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0
[6] org.Mm.eg.db_3.4.0
[7] Homo.sapiens_1.3.1
[8] GO.db_3.4.0
[9] OrganismDbi_1.17.1
[10] org.Hs.eg.db_3.4.0
[11] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[12] org.Dm.eg.db_3.4.0
[13] TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.3.0
[14] GenomicFeatures_1.27.2
[15] AnnotationDbi_1.37.0
[16] Biobase_2.35.0
[17] GenomicRanges_1.27.6
[18] GenomeInfoDb_1.11.4
[19] IRanges_2.9.8
[20] S4Vectors_0.13.2
[21] BiocGenerics_0.21.0
[22] BiocInstaller_1.25.2
loaded via a namespace (and not attached):
[1] compiler_3.4.0 XVector_0.15.0
[3] bitops_1.0-6 tools_3.4.0
[5] zlibbioc_1.21.0biomaRt_2.31.1
[7] RSQLite_1.0.0 lattice_0.20-34
[9] Matrix_1.2-7.1 graph_1.53.0
[11] DBI_0.5-1 rtracklayer_1.35.1
[13] Biostrings_2.43.0 grid_3.4.0
[15] XML_3.98-1.5 RBGL_1.51.0
[17] BiocParallel_1.9.1 Rsamtools_1.27.2
[19] GenomicAlignments_1.11.1 SummarizedExperiment_1.5.3
[21] RCurl_1.95-4.8
>
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
This email message may contain legally privileged and/or confidential
information. If you are not the intended recipient(s), or the employee or
agent responsible for the delivery of this message to the intended
recipient(s), you are hereby notified that any disclosure, copying,
distribution, or use of this email message is prohibited. If you have received
this message in error, please notify the sender immediately by e-mail and
delete this email message from your computer. Thank you.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
This email
Re: [Bioc-devel] OrganismDb package for Drosophila.melanogaster
On 11/15/2016 02:34 PM, Martin Morgan wrote:
On 11/15/2016 09:52 AM, Obenchain, Valerie wrote:
Hi Pariksheet,
On 11/15/2016 03:32 AM, Pariksheet Nanda wrote:
Hi folks,
It would be great to have an OrganismDb package for
Drosophila.melanogaster, similar to Homo.sapiens, Mus.musculus and
Rattus.norvegicus.
While trying to do this on my own using the Homo.sapiens package as a
starting point, I found the most similar looking keys to relate
org.Dm.eg.db and TxDb.Dmelanogaster.UCSC.dm6.ensGene to be "ENSEMBL" and
"GENEID" though there's a ".1" tacked to the end "GENEID" which makes it
harder to supply the graphInfo object to
OrganismDbi:::.loadOrganismDbiPkg:
!> key_ <- function(db, key) sort(as.character(
+select(db, keys(db, key), key,
key)[[key]]))
> key_head <- function(db, key) head(key_(db, key))
> key_head(TxDb.Dmelanogaster.UCSC.dm6.ensGene, "GENEID")
'select()' returned 1:1 mapping between keys and columns
[1] "FBgn003.1" "FBgn008.1" "FBgn014.1" "FBgn015.1"
[5] "FBgn017.1" "FBgn018.1"
> key_head(org.Dm.eg.db, "ENSEMBL")
[1] "FBgn008" "FBgn014" "FBgn015" "FBgn017"
"FBgn018"
[6] "FBgn022"
>
In other words, like Rattus.norvegicus, it might be good do add a UCSC
"refGene" TxDb package for dm6 as "ensGene" doesn't appear to be as
good of
a candidate (at least without some ugliness)? I was looking at
creating a
dm6 UCSC "refGene" TxDb.
You can use GenomicFeatures::makeTxDbFromUCSC() to create the TxDb. The
man page, ?makeTxDbFromUCSC, also has helper functions that display
available genomes, tables and tracks.
I'm not completely sure of the result, but
library(OrganismDb)
odb = makeOrganismDbFromUCSC("dm6", tableName="refGene")
^^tablename
might be most of the way there?
Martin
Valerie
I imagine one would query the UCSC public MySQL
server and then do the SQLite conversion. Although the conversion to
SQLite seems a bit finagly as the datatypes differ between MySQL and
SQLite
and I'm having a hard time finding a well supported tool to do it; I
don't
want to introduce errors or harm reproducibility. What do you use for
MySQL to SQLite conversion? Or would it be more sensible for you
benevolent dictators to generate the package(s)?
Pariksheet
---
Pariksheet Nanda
PhD Candidate in Genetics and Genomics
System Administrator, Storrs HPC Cluster
University of Connecticut
---
> sessionInfo()
R Under development (unstable) (2016-11-13 r71655)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_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] stats4parallel stats graphics grDevices utils
datasets
[8] methods base
other attached packages:
[1] Rattus.norvegicus_1.3.1
[2] TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.0
[3] org.Rn.eg.db_3.4.0
[4] Mus.musculus_1.3.1
[5] TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0
[6] org.Mm.eg.db_3.4.0
[7] Homo.sapiens_1.3.1
[8] GO.db_3.4.0
[9] OrganismDbi_1.17.1
[10] org.Hs.eg.db_3.4.0
[11] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[12] org.Dm.eg.db_3.4.0
[13] TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.3.0
[14] GenomicFeatures_1.27.2
[15] AnnotationDbi_1.37.0
[16] Biobase_2.35.0
[17] GenomicRanges_1.27.6
[18] GenomeInfoDb_1.11.4
[19] IRanges_2.9.8
[20] S4Vectors_0.13.2
[21] BiocGenerics_0.21.0
[22] BiocInstaller_1.25.2
loaded via a namespace (and not attached):
[1] compiler_3.4.0 XVector_0.15.0
[3] bitops_1.0-6 tools_3.4.0
[5] zlibbioc_1.21.0biomaRt_2.31.1
[7] RSQLite_1.0.0 lattice_0.20-34
[9] Matrix_1.2-7.1 graph_1.53.0
[11] DBI_0.5-1 rtracklayer_1.35.1
[13] Biostrings_2.43.0 grid_3.4.0
[15] XML_3.98-1.5 RBGL_1.51.0
[17] BiocParallel_1.9.1 Rsamtools_1.27.2
[19] GenomicAlignments_1.11.1 SummarizedExperiment_1.5.3
[21] RCurl_1.95-4.8
>
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
This email message may contain legally privileged and/or confidential
information. If you are not the intended recipient(s), or the
employee or agent responsible for the delivery of this message to the
intended recipient(s), you are hereby notified that any disclosure,
copying, distribution, or use of this email message is prohibited. If
you have received this message in error, please notify the sender
immediately by e-mail and delete this email message from your
computer. Thank you.
___
Re: [Bioc-devel] OrganismDb package for Drosophila.melanogaster
Hi Pariksheet, On 11/15/2016 03:32 AM, Pariksheet Nanda wrote: > Hi folks, > > It would be great to have an OrganismDb package for > Drosophila.melanogaster, similar to Homo.sapiens, Mus.musculus and > Rattus.norvegicus. > > While trying to do this on my own using the Homo.sapiens package as a > starting point, I found the most similar looking keys to relate > org.Dm.eg.db and TxDb.Dmelanogaster.UCSC.dm6.ensGene to be "ENSEMBL" and > "GENEID" though there's a ".1" tacked to the end "GENEID" which makes it > harder to supply the graphInfo object to OrganismDbi:::.loadOrganismDbiPkg: > > !> key_ <- function(db, key) sort(as.character( > +select(db, keys(db, key), key, > key)[[key]])) > > key_head <- function(db, key) head(key_(db, key)) > > key_head(TxDb.Dmelanogaster.UCSC.dm6.ensGene, "GENEID") > 'select()' returned 1:1 mapping between keys and columns > [1] "FBgn003.1" "FBgn008.1" "FBgn014.1" "FBgn015.1" > [5] "FBgn017.1" "FBgn018.1" > > key_head(org.Dm.eg.db, "ENSEMBL") > [1] "FBgn008" "FBgn014" "FBgn015" "FBgn017" "FBgn018" > [6] "FBgn022" > > > > In other words, like Rattus.norvegicus, it might be good do add a UCSC > "refGene" TxDb package for dm6 as "ensGene" doesn't appear to be as good of > a candidate (at least without some ugliness)? I was looking at creating a > dm6 UCSC "refGene" TxDb. You can use GenomicFeatures::makeTxDbFromUCSC() to create the TxDb. The man page, ?makeTxDbFromUCSC, also has helper functions that display available genomes, tables and tracks. Valerie > I imagine one would query the UCSC public MySQL > server and then do the SQLite conversion. Although the conversion to > SQLite seems a bit finagly as the datatypes differ between MySQL and SQLite > and I'm having a hard time finding a well supported tool to do it; I don't > want to introduce errors or harm reproducibility. What do you use for > MySQL to SQLite conversion? Or would it be more sensible for you > benevolent dictators to generate the package(s)? > > Pariksheet > > --- > Pariksheet Nanda > PhD Candidate in Genetics and Genomics > System Administrator, Storrs HPC Cluster > University of Connecticut > > --- > > sessionInfo() > R Under development (unstable) (2016-11-13 r71655) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Ubuntu 16.04.1 LTS > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8LC_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] stats4parallel stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] Rattus.norvegicus_1.3.1 > [2] TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.0 > [3] org.Rn.eg.db_3.4.0 > [4] Mus.musculus_1.3.1 > [5] TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 > [6] org.Mm.eg.db_3.4.0 > [7] Homo.sapiens_1.3.1 > [8] GO.db_3.4.0 > [9] OrganismDbi_1.17.1 > [10] org.Hs.eg.db_3.4.0 > [11] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 > [12] org.Dm.eg.db_3.4.0 > [13] TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.3.0 > [14] GenomicFeatures_1.27.2 > [15] AnnotationDbi_1.37.0 > [16] Biobase_2.35.0 > [17] GenomicRanges_1.27.6 > [18] GenomeInfoDb_1.11.4 > [19] IRanges_2.9.8 > [20] S4Vectors_0.13.2 > [21] BiocGenerics_0.21.0 > [22] BiocInstaller_1.25.2 > > loaded via a namespace (and not attached): > [1] compiler_3.4.0 XVector_0.15.0 > [3] bitops_1.0-6 tools_3.4.0 > [5] zlibbioc_1.21.0biomaRt_2.31.1 > [7] RSQLite_1.0.0 lattice_0.20-34 > [9] Matrix_1.2-7.1 graph_1.53.0 > [11] DBI_0.5-1 rtracklayer_1.35.1 > [13] Biostrings_2.43.0 grid_3.4.0 > [15] XML_3.98-1.5 RBGL_1.51.0 > [17] BiocParallel_1.9.1 Rsamtools_1.27.2 > [19] GenomicAlignments_1.11.1 SummarizedExperiment_1.5.3 > [21] RCurl_1.95-4.8 > > > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] OrganismDb package for Drosophila.melanogaster
Hi folks, It would be great to have an OrganismDb package for Drosophila.melanogaster, similar to Homo.sapiens, Mus.musculus and Rattus.norvegicus. While trying to do this on my own using the Homo.sapiens package as a starting point, I found the most similar looking keys to relate org.Dm.eg.db and TxDb.Dmelanogaster.UCSC.dm6.ensGene to be "ENSEMBL" and "GENEID" though there's a ".1" tacked to the end "GENEID" which makes it harder to supply the graphInfo object to OrganismDbi:::.loadOrganismDbiPkg: !> key_ <- function(db, key) sort(as.character( +select(db, keys(db, key), key, key)[[key]])) > key_head <- function(db, key) head(key_(db, key)) > key_head(TxDb.Dmelanogaster.UCSC.dm6.ensGene, "GENEID") 'select()' returned 1:1 mapping between keys and columns [1] "FBgn003.1" "FBgn008.1" "FBgn014.1" "FBgn015.1" [5] "FBgn017.1" "FBgn018.1" > key_head(org.Dm.eg.db, "ENSEMBL") [1] "FBgn008" "FBgn014" "FBgn015" "FBgn017" "FBgn018" [6] "FBgn022" > In other words, like Rattus.norvegicus, it might be good do add a UCSC "refGene" TxDb package for dm6 as "ensGene" doesn't appear to be as good of a candidate (at least without some ugliness)? I was looking at creating a dm6 UCSC "refGene" TxDb. I imagine one would query the UCSC public MySQL server and then do the SQLite conversion. Although the conversion to SQLite seems a bit finagly as the datatypes differ between MySQL and SQLite and I'm having a hard time finding a well supported tool to do it; I don't want to introduce errors or harm reproducibility. What do you use for MySQL to SQLite conversion? Or would it be more sensible for you benevolent dictators to generate the package(s)? Pariksheet --- Pariksheet Nanda PhD Candidate in Genetics and Genomics System Administrator, Storrs HPC Cluster University of Connecticut --- > sessionInfo() R Under development (unstable) (2016-11-13 r71655) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.1 LTS locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_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] stats4parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] Rattus.norvegicus_1.3.1 [2] TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.0 [3] org.Rn.eg.db_3.4.0 [4] Mus.musculus_1.3.1 [5] TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 [6] org.Mm.eg.db_3.4.0 [7] Homo.sapiens_1.3.1 [8] GO.db_3.4.0 [9] OrganismDbi_1.17.1 [10] org.Hs.eg.db_3.4.0 [11] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 [12] org.Dm.eg.db_3.4.0 [13] TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.3.0 [14] GenomicFeatures_1.27.2 [15] AnnotationDbi_1.37.0 [16] Biobase_2.35.0 [17] GenomicRanges_1.27.6 [18] GenomeInfoDb_1.11.4 [19] IRanges_2.9.8 [20] S4Vectors_0.13.2 [21] BiocGenerics_0.21.0 [22] BiocInstaller_1.25.2 loaded via a namespace (and not attached): [1] compiler_3.4.0 XVector_0.15.0 [3] bitops_1.0-6 tools_3.4.0 [5] zlibbioc_1.21.0biomaRt_2.31.1 [7] RSQLite_1.0.0 lattice_0.20-34 [9] Matrix_1.2-7.1 graph_1.53.0 [11] DBI_0.5-1 rtracklayer_1.35.1 [13] Biostrings_2.43.0 grid_3.4.0 [15] XML_3.98-1.5 RBGL_1.51.0 [17] BiocParallel_1.9.1 Rsamtools_1.27.2 [19] GenomicAlignments_1.11.1 SummarizedExperiment_1.5.3 [21] RCurl_1.95-4.8 > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
