how to unlock a package environment

Question: how to unlock a package environment

10.1 years ago by

Hi all, I am currently analyzing some arabidopsis thaliana experiments (ath1121501 GeneChip) The corresponding annotation package, ath1121501.db, is a little bit 'special' as there is no ENTREZID map for the chip. I would like to cheat and create a fake ath1121501ENTREZID for the environment as a copied instance of ath1121501ACCNUM (in order to use, for instance, the genefilter package's function "nsFilter" to deal with non annotated, or duplicated probesets) The problem is that I am not able to create a new entry in the package:ath112150.db as it is a locked environment. Is there any way to temporarily unlock it, do some stuff and lock it again? (It seems easy to lock environments, using the lockEnvironment function, but I did not find an easy way to unlock them) Thanks in advance Ariel./ -- Dr. Ariel Chernomoretz Departamento de Fisica, FCEyN, Universidad de Buenos Aires, (1428) Ciudad Universitaria, Ciudad de Buenos Aires, Argentina. TE +54 11 4576 3390 ext 817 Fax +54 11 4576 3357 email: ariel@df.uba.ar Webpage: http://www.df.uba.ar/users/ariel [[alternative HTML version deleted]]

annotation arabidopsis thaliana ath1121501 genefilter • 948 views

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modified 10.1 years ago by Marc Carlson • 7.2k • written 10.1 years ago by Ariel Chernomoretz • 160

Answer: how to unlock a package environment

10.1 years ago by

Hervé Pagès ♦♦ 14k

United States

Hervé Pagès ♦♦ 14k wrote:

Hi Ariel, One solution is that you use the development version of Bioconductor (BioC 2.5, to be released soon, based on the R-2.10 series). In the development version of genefilter it looks like the nsFilter() function has been improved in order to deal properly with the peculiarity of the ath1121501.db package. Internally it's now calling a little helper function .findCentralID() (not exported) in order to determine what's the central ID in the annotation package: library(genefilter) library(hgu95av2.db) library(ath1121501.db) > genefilter:::.findCentralID("hgu95av2") [1] "ENTREZID" > genefilter:::.findCentralID("ath1121501") [1] "ACCNUM" Cheers, H. Ariel Chernomoretz wrote: > Hi all, > I am currently analyzing some arabidopsis thaliana experiments (ath1121501 > GeneChip) > The corresponding annotation package, ath1121501.db, is a little bit > 'special' as > there is no ENTREZID map for the chip. > I would like to cheat and create a fake ath1121501ENTREZID for the > environment as a copied instance of ath1121501ACCNUM (in order to use, for > instance, the genefilter package's function "nsFilter" to deal with non > annotated, or duplicated probesets) > > The problem is that I am not able to create a new entry in the > package:ath112150.db as it is a locked environment. Is there any way to > temporarily unlock it, do some stuff and lock it again? > (It seems easy to lock environments, using the lockEnvironment function, but > I did not find an easy way to unlock them) > > Thanks in advance > Ariel./ > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319

ADD COMMENT • link written 10.1 years ago by Hervé Pagès ♦♦ 14k

Forgot to send my sessionInfo(), sorry: > sessionInfo() R version 2.10.0 Under development (unstable) (2009-09-24 r49817) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_CA.UTF-8 [7] LC_PAPER=en_CA.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hgu95av2.db_2.3.5 org.Hs.eg.db_2.3.5 genefilter_1.25.9 [4] ath1121501.db_2.3.5 org.At.tair.db_2.3.5 RSQLite_0.7-2 [7] DBI_0.2-4 AnnotationDbi_1.7.17 Biobase_2.5.8 loaded via a namespace (and not attached): [1] annotate_1.23.4 splines_2.10.0 survival_2.35-7 tools_2.10.0 [5] xtable_1.5-5 H. Hervé Pagès wrote: > Hi Ariel, > > One solution is that you use the development version of Bioconductor > (BioC 2.5, to be released soon, based on the R-2.10 series). > > In the development version of genefilter it looks like the nsFilter() > function has been improved in order to deal properly with the > peculiarity of the ath1121501.db package. Internally it's now > calling a little helper function .findCentralID() (not exported) > in order to determine what's the central ID in the annotation > package: > > library(genefilter) > library(hgu95av2.db) > library(ath1121501.db) > > genefilter:::.findCentralID("hgu95av2") > [1] "ENTREZID" > > genefilter:::.findCentralID("ath1121501") > [1] "ACCNUM" > > Cheers, > H. > > > Ariel Chernomoretz wrote: >> Hi all, >> I am currently analyzing some arabidopsis thaliana experiments >> (ath1121501 >> GeneChip) >> The corresponding annotation package, ath1121501.db, is a little bit >> 'special' as >> there is no ENTREZID map for the chip. >> I would like to cheat and create a fake ath1121501ENTREZID for the >> environment as a copied instance of ath1121501ACCNUM (in order to use, >> for >> instance, the genefilter package's function "nsFilter" to deal with non >> annotated, or duplicated probesets) >> >> The problem is that I am not able to create a new entry in the >> package:ath112150.db as it is a locked environment. Is there any way to >> temporarily unlock it, do some stuff and lock it again? >> (It seems easy to lock environments, using the lockEnvironment >> function, but >> I did not find an easy way to unlock them) >> >> Thanks in advance >> Ariel./ >> > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319

ADD REPLY • link written 10.1 years ago by Hervé Pagès ♦♦ 14k

Excelent news... (I noticed that there is an 'org.At.tair.db' also available in the devel version!) Thanks Herve for the info A./ PS: I am still curious about the locking/unlocking issue... 2009/10/1 Hervé Pagès <hpages@fhcrc.org> > Forgot to send my sessionInfo(), sorry: > > > sessionInfo() > R version 2.10.0 Under development (unstable) (2009-09-24 r49817) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_CA.UTF-8 > [7] LC_PAPER=en_CA.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] hgu95av2.db_2.3.5 org.Hs.eg.db_2.3.5 genefilter_1.25.9 > [4] ath1121501.db_2.3.5 org.At.tair.db_2.3.5 RSQLite_0.7-2 > [7] DBI_0.2-4 AnnotationDbi_1.7.17 Biobase_2.5.8 > > loaded via a namespace (and not attached): > [1] annotate_1.23.4 splines_2.10.0 survival_2.35-7 tools_2.10.0 > [5] xtable_1.5-5 > > > H. > > > > Hervé Pagès wrote: > >> Hi Ariel, >> >> One solution is that you use the development version of Bioconductor >> (BioC 2.5, to be released soon, based on the R-2.10 series). >> >> In the development version of genefilter it looks like the nsFilter() >> function has been improved in order to deal properly with the >> peculiarity of the ath1121501.db package. Internally it's now >> calling a little helper function .findCentralID() (not exported) >> in order to determine what's the central ID in the annotation >> package: >> >> library(genefilter) >> library(hgu95av2.db) >> library(ath1121501.db) >> > genefilter:::.findCentralID("hgu95av2") >> [1] "ENTREZID" >> > genefilter:::.findCentralID("ath1121501") >> [1] "ACCNUM" >> >> Cheers, >> H. >> >> >> Ariel Chernomoretz wrote: >> >>> Hi all, >>> I am currently analyzing some arabidopsis thaliana experiments >>> (ath1121501 >>> GeneChip) >>> The corresponding annotation package, ath1121501.db, is a little bit >>> 'special' as >>> there is no ENTREZID map for the chip. >>> I would like to cheat and create a fake ath1121501ENTREZID for the >>> environment as a copied instance of ath1121501ACCNUM (in order to use, >>> for >>> instance, the genefilter package's function "nsFilter" to deal with non >>> annotated, or duplicated probesets) >>> >>> The problem is that I am not able to create a new entry in the >>> package:ath112150.db as it is a locked environment. Is there any way to >>> temporarily unlock it, do some stuff and lock it again? >>> (It seems easy to lock environments, using the lockEnvironment function, >>> but >>> I did not find an easy way to unlock them) >>> >>> Thanks in advance >>> Ariel./ >>> >>> >> > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M2-B876 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages@fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > -- Dr. Ariel Chernomoretz Departamento de Fisica, FCEyN, Universidad de Buenos Aires, (1428) Ciudad Universitaria, Ciudad de Buenos Aires, Argentina. TE +54 11 4576 3390 ext 817 Fax +54 11 4576 3357 email: ariel@df.uba.ar Webpage: http://www.df.uba.ar/users/ariel [[alternative HTML version deleted]]

ADD REPLY • link written 10.1 years ago by Ariel Chernomoretz • 160

Answer: how to unlock a package environment

10.1 years ago by

Marc Carlson • 7.2k

United States

Marc Carlson • 7.2k wrote:

Hi Ariel, The reason why the arabidopsis chip packages do not have an ENTREZID mapping is because this is not what these packages are primarily based upon and we didn't want people to grab those IDs out of habit from using the other chip packages. Instead, these packages are based on the "TAIR" sources which are popular with the community that likes to study Arabidopsis. As a result of this, the mapping that you want to use to filter the results should be the TAIR IDs which for historical reasons live in the ACCNUM mapping for the arabidopsis packages. Herve beat me to the punch, but the nsFilter method in the latest version of the devel branch has already been modified to determine what kind of annotation package you are using and then make the correct decision about what kind of mapping it should be using to filter. If you really want entrez gene IDs for something else, you can get them by using the ENTREZID mapping found in the org.At.tair.db package. All of the TAIR IDs from your chip package should have a match in that package which is also primarily based on the TAIR data sources. I have made a change to the release version of this package to correct this bug, it should show up online within about a day. As for unlocking the packages, we strongly discourage that as it can cause all manner of odd behavior with other packages that depend on these annotations to produce standard annotations... But if you really want to play with "bombs and guns", you should be able to set the database file to be write-able. Marc Ariel Chernomoretz wrote: > Hi all, > I am currently analyzing some arabidopsis thaliana experiments (ath1121501 > GeneChip) > The corresponding annotation package, ath1121501.db, is a little bit > 'special' as > there is no ENTREZID map for the chip. > I would like to cheat and create a fake ath1121501ENTREZID for the > environment as a copied instance of ath1121501ACCNUM (in order to use, for > instance, the genefilter package's function "nsFilter" to deal with non > annotated, or duplicated probesets) > > The problem is that I am not able to create a new entry in the > package:ath112150.db as it is a locked environment. Is there any way to > temporarily unlock it, do some stuff and lock it again? > (It seems easy to lock environments, using the lockEnvironment function, but > I did not find an easy way to unlock them) > > Thanks in advance > Ariel./ > >

ADD COMMENT • link written 10.1 years ago by Marc Carlson • 7.2k

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