Re: [Bioc-devel] mapIds methods for ExpressionSet and SummarizedExperiment
Dear Martin, I finally found the time to make the code available via GitHub: https://github.com/lgeistlinger/MapIds and added you as a collaborator. This is currently just a quick put-together for you to get an impression. NA and duplicated mappings currently need to be removed to ensure uniqueness of featureNames and rownames, respectively (via na.rm=TRUE and dupl.rm=TRUE). But there are, of course, other/better ways to summarize over NA's/Duplicates, e.g. by appropriately passing that on to the 'multiVals' Argument of AnnotationDbi::mapIds(). Just let me know in case you find that of any use or you find things that could be improved/extended. Best, Ludwig --- Dear Martin, Ok, I am tyding that up and provide that via GitHub for you. BTW, these ranges to Ids and vice versa sounds very cool! > The original intention of the annotation() slot in ExpressionSet was to > include the microarray chip identifier, so that one references this when > translating from probeset to gene identifiers. One question to that, as I often find my functions to ask for the organism uder study (which I believe is actually most typically known when investigating an expression dataset). While there are convenient ways to ask microarray annotation packages for the organism under study (and thus infer it from annotation(eset)), I wonder whether there is a similar slot for SummarizedExperiment, eg an 'organism' slot? Or are there specific reasons arguing against that? Best, Ludwig > Hi Ludwig -- > > It would be really great to see what you've put together; can you make > your code available somewhere, maybe via github? > > I think the facilities already in Bioconductor include: > > - select() and the OrganismDb (e.g., Homo.sapiens) packages > > - (Recently introduced, in bioc-devel) GenomicFeatures::mapIds() > > - GSEABase mapIdentifiers() > > - The AnnotationFuncs package (some of this functionality might be > redundant with select() / mapIds(); maybe your idea is a more refined > version of this? > > - biomaRt, including the relatively under-known use of select() with mart > objects. > > I think a particularly valuable development (initial implementation in > GenomicFeatures::mapIds()) is transparent mapping to / from genomic > ranges. > > The original intention of the annotation() slot in ExpressionSet was to > include the microarray chip identifier, so that one references this when > translating from probeset to gene identifiers. > > Martin > > From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Ludwig > Geistlinger [ludwig.geistlin...@bio.ifi.lmu.de] > Sent: Thursday, December 17, 2015 5:05 AM > To: bioc-devel@r-project.org > Subject: [Bioc-devel] mapIds methods for ExpressionSet and > SummarizedExperiment > > Dear Bioc Team, > > I have implemented mapIds methods mapping featureNames (ExpressionSet) and > rownames (SummarizedExperiment) between major gene ID types such as > ENSEMBL and ENTREZ by passing that on AnnotationDbi::mapIds. > > Given an ExpressionSet/SummarizedExperiment and an organism under > investigation such as 'Homo sapiens', the methods are checking whether the > corresponding org.db package is available, otherwise the package is > automatically installed and loaded. > Subsequently, the featureNames/rownames are mapped from the specified > from.id.type to the desired to.id.type, corresponding to keytypes of the > org.db package. > Options to deal with NA and duplicate mappings are also provided in order > to ensure that featureNames/rownames are unique after the mapping. > > Advantage is that end users do not require knowledge of the Bioc > annotation infrastructure, but rather just need to provide the organism > under investigation in a convenient format also for non-Biocs. > > I have not found something similar in existing packages and I am wondering > whether this could be something of general interest. > > Best, > Ludwig > > -- > Dipl.-Bioinf. Ludwig Geistlinger > > Lehr- und Forschungseinheit für Bioinformatik > Institut für Informatik > Ludwig-Maximilians-Universität München > Amalienstrasse 17, 2. Stock, Büro A201 > 80333 München > > Tel.: 089-2180-4067 > eMail: ludwig.geistlin...@bio.ifi.lmu.de > > ___ > 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
Re: [Bioc-devel] mapIds methods for ExpressionSet and SummarizedExperiment
Thanks Ludwig I'll have a look. Martin From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Ludwig Geistlinger [ludwig.geistlin...@bio.ifi.lmu.de] Sent: Wednesday, January 06, 2016 12:07 PM To: bioc-devel@r-project.org Subject: Re: [Bioc-devel] mapIds methods for ExpressionSet and SummarizedExperiment Dear Martin, I finally found the time to make the code available via GitHub: https://github.com/lgeistlinger/MapIds and added you as a collaborator. This is currently just a quick put-together for you to get an impression. NA and duplicated mappings currently need to be removed to ensure uniqueness of featureNames and rownames, respectively (via na.rm=TRUE and dupl.rm=TRUE). But there are, of course, other/better ways to summarize over NA's/Duplicates, e.g. by appropriately passing that on to the 'multiVals' Argument of AnnotationDbi::mapIds(). Just let me know in case you find that of any use or you find things that could be improved/extended. Best, Ludwig --- Dear Martin, Ok, I am tyding that up and provide that via GitHub for you. BTW, these ranges to Ids and vice versa sounds very cool! > The original intention of the annotation() slot in ExpressionSet was to > include the microarray chip identifier, so that one references this when > translating from probeset to gene identifiers. One question to that, as I often find my functions to ask for the organism uder study (which I believe is actually most typically known when investigating an expression dataset). While there are convenient ways to ask microarray annotation packages for the organism under study (and thus infer it from annotation(eset)), I wonder whether there is a similar slot for SummarizedExperiment, eg an 'organism' slot? Or are there specific reasons arguing against that? Best, Ludwig > Hi Ludwig -- > > It would be really great to see what you've put together; can you make > your code available somewhere, maybe via github? > > I think the facilities already in Bioconductor include: > > - select() and the OrganismDb (e.g., Homo.sapiens) packages > > - (Recently introduced, in bioc-devel) GenomicFeatures::mapIds() > > - GSEABase mapIdentifiers() > > - The AnnotationFuncs package (some of this functionality might be > redundant with select() / mapIds(); maybe your idea is a more refined > version of this? > > - biomaRt, including the relatively under-known use of select() with mart > objects. > > I think a particularly valuable development (initial implementation in > GenomicFeatures::mapIds()) is transparent mapping to / from genomic > ranges. > > The original intention of the annotation() slot in ExpressionSet was to > include the microarray chip identifier, so that one references this when > translating from probeset to gene identifiers. > > Martin > > From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Ludwig > Geistlinger [ludwig.geistlin...@bio.ifi.lmu.de] > Sent: Thursday, December 17, 2015 5:05 AM > To: bioc-devel@r-project.org > Subject: [Bioc-devel] mapIds methods for ExpressionSet and > SummarizedExperiment > > Dear Bioc Team, > > I have implemented mapIds methods mapping featureNames (ExpressionSet) and > rownames (SummarizedExperiment) between major gene ID types such as > ENSEMBL and ENTREZ by passing that on AnnotationDbi::mapIds. > > Given an ExpressionSet/SummarizedExperiment and an organism under > investigation such as 'Homo sapiens', the methods are checking whether the > corresponding org.db package is available, otherwise the package is > automatically installed and loaded. > Subsequently, the featureNames/rownames are mapped from the specified > from.id.type to the desired to.id.type, corresponding to keytypes of the > org.db package. > Options to deal with NA and duplicate mappings are also provided in order > to ensure that featureNames/rownames are unique after the mapping. > > Advantage is that end users do not require knowledge of the Bioc > annotation infrastructure, but rather just need to provide the organism > under investigation in a convenient format also for non-Biocs. > > I have not found something similar in existing packages and I am wondering > whether this could be something of general interest. > > Best, > Ludwig > > -- > Dipl.-Bioinf. Ludwig Geistlinger > > Lehr- und Forschungseinheit für Bioinformatik > Institut für Informatik > Ludwig-Maximilians-Universität München > Amalienstrasse 17, 2. Stock, Büro A201 > 80333 München > > Tel.: 089-2180-4067 > eMail: ludwig.geistlin...@bio.ifi.lmu.de > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > >
Re: [Bioc-devel] mapIds methods for ExpressionSet and SummarizedExperiment
Dear Martin, Ok, I am tyding that up and provide that via GitHub for you. BTW, these ranges to Ids and vice versa sounds very cool! > The original intention of the annotation() slot in ExpressionSet was to > include the microarray chip identifier, so that one references this when > translating from probeset to gene identifiers. One question to that, as I often find my functions to ask for the organism uder study (which I believe is actually most typically known when investigating an expression dataset). While there are convenient ways to ask microarray annotation packages for the organism under study (and thus infer it from annotation(eset)), I wonder whether there is a similar slot for SummarizedExperiment, eg an 'organism' slot? Or are there specific reasons arguing against that? Best, Ludwig > Hi Ludwig -- > > It would be really great to see what you've put together; can you make > your code available somewhere, maybe via github? > > I think the facilities already in Bioconductor include: > > - select() and the OrganismDb (e.g., Homo.sapiens) packages > > - (Recently introduced, in bioc-devel) GenomicFeatures::mapIds() > > - GSEABase mapIdentifiers() > > - The AnnotationFuncs package (some of this functionality might be > redundant with select() / mapIds(); maybe your idea is a more refined > version of this? > > - biomaRt, including the relatively under-known use of select() with mart > objects. > > I think a particularly valuable development (initial implementation in > GenomicFeatures::mapIds()) is transparent mapping to / from genomic > ranges. > > The original intention of the annotation() slot in ExpressionSet was to > include the microarray chip identifier, so that one references this when > translating from probeset to gene identifiers. > > Martin > > From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Ludwig > Geistlinger [ludwig.geistlin...@bio.ifi.lmu.de] > Sent: Thursday, December 17, 2015 5:05 AM > To: bioc-devel@r-project.org > Subject: [Bioc-devel] mapIds methods for ExpressionSet and > SummarizedExperiment > > Dear Bioc Team, > > I have implemented mapIds methods mapping featureNames (ExpressionSet) and > rownames (SummarizedExperiment) between major gene ID types such as > ENSEMBL and ENTREZ by passing that on AnnotationDbi::mapIds. > > Given an ExpressionSet/SummarizedExperiment and an organism under > investigation such as 'Homo sapiens', the methods are checking whether the > corresponding org.db package is available, otherwise the package is > automatically installed and loaded. > Subsequently, the featureNames/rownames are mapped from the specified > from.id.type to the desired to.id.type, corresponding to keytypes of the > org.db package. > Options to deal with NA and duplicate mappings are also provided in order > to ensure that featureNames/rownames are unique after the mapping. > > Advantage is that end users do not require knowledge of the Bioc > annotation infrastructure, but rather just need to provide the organism > under investigation in a convenient format also for non-Biocs. > > I have not found something similar in existing packages and I am wondering > whether this could be something of general interest. > > Best, > Ludwig > > -- > Dipl.-Bioinf. Ludwig Geistlinger > > Lehr- und Forschungseinheit für Bioinformatik > Institut für Informatik > Ludwig-Maximilians-Universität München > Amalienstrasse 17, 2. Stock, Büro A201 > 80333 München > > Tel.: 089-2180-4067 > eMail: ludwig.geistlin...@bio.ifi.lmu.de > > ___ > 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. > -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] mapIds methods for ExpressionSet and SummarizedExperiment
Hi Ludwig -- It would be really great to see what you've put together; can you make your code available somewhere, maybe via github? I think the facilities already in Bioconductor include: - select() and the OrganismDb (e.g., Homo.sapiens) packages - (Recently introduced, in bioc-devel) GenomicFeatures::mapIds() - GSEABase mapIdentifiers() - The AnnotationFuncs package (some of this functionality might be redundant with select() / mapIds(); maybe your idea is a more refined version of this? - biomaRt, including the relatively under-known use of select() with mart objects. I think a particularly valuable development (initial implementation in GenomicFeatures::mapIds()) is transparent mapping to / from genomic ranges. The original intention of the annotation() slot in ExpressionSet was to include the microarray chip identifier, so that one references this when translating from probeset to gene identifiers. Martin From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Ludwig Geistlinger [ludwig.geistlin...@bio.ifi.lmu.de] Sent: Thursday, December 17, 2015 5:05 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] mapIds methods for ExpressionSet and SummarizedExperiment Dear Bioc Team, I have implemented mapIds methods mapping featureNames (ExpressionSet) and rownames (SummarizedExperiment) between major gene ID types such as ENSEMBL and ENTREZ by passing that on AnnotationDbi::mapIds. Given an ExpressionSet/SummarizedExperiment and an organism under investigation such as 'Homo sapiens', the methods are checking whether the corresponding org.db package is available, otherwise the package is automatically installed and loaded. Subsequently, the featureNames/rownames are mapped from the specified from.id.type to the desired to.id.type, corresponding to keytypes of the org.db package. Options to deal with NA and duplicate mappings are also provided in order to ensure that featureNames/rownames are unique after the mapping. Advantage is that end users do not require knowledge of the Bioc annotation infrastructure, but rather just need to provide the organism under investigation in a convenient format also for non-Biocs. I have not found something similar in existing packages and I am wondering whether this could be something of general interest. Best, Ludwig -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ 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
Re: [Bioc-devel] mapIds methods for ExpressionSet and SummarizedExperiment
Oops, those newly added functions in GenomicFeatures are GenomicFeatures::mapRangesToIds GenomicFeatures::mapIdsToRanges Martin From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Morgan, Martin [martin.mor...@roswellpark.org] Sent: Friday, December 18, 2015 1:15 PM To: Ludwig Geistlinger; bioc-devel@r-project.org Subject: Re: [Bioc-devel] mapIds methods for ExpressionSet and SummarizedExperiment Hi Ludwig -- It would be really great to see what you've put together; can you make your code available somewhere, maybe via github? I think the facilities already in Bioconductor include: - select() and the OrganismDb (e.g., Homo.sapiens) packages - (Recently introduced, in bioc-devel) GenomicFeatures::mapIds() - GSEABase mapIdentifiers() - The AnnotationFuncs package (some of this functionality might be redundant with select() / mapIds(); maybe your idea is a more refined version of this? - biomaRt, including the relatively under-known use of select() with mart objects. I think a particularly valuable development (initial implementation in GenomicFeatures::mapIds()) is transparent mapping to / from genomic ranges. The original intention of the annotation() slot in ExpressionSet was to include the microarray chip identifier, so that one references this when translating from probeset to gene identifiers. Martin From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Ludwig Geistlinger [ludwig.geistlin...@bio.ifi.lmu.de] Sent: Thursday, December 17, 2015 5:05 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] mapIds methods for ExpressionSet and SummarizedExperiment Dear Bioc Team, I have implemented mapIds methods mapping featureNames (ExpressionSet) and rownames (SummarizedExperiment) between major gene ID types such as ENSEMBL and ENTREZ by passing that on AnnotationDbi::mapIds. Given an ExpressionSet/SummarizedExperiment and an organism under investigation such as 'Homo sapiens', the methods are checking whether the corresponding org.db package is available, otherwise the package is automatically installed and loaded. Subsequently, the featureNames/rownames are mapped from the specified from.id.type to the desired to.id.type, corresponding to keytypes of the org.db package. Options to deal with NA and duplicate mappings are also provided in order to ensure that featureNames/rownames are unique after the mapping. Advantage is that end users do not require knowledge of the Bioc annotation infrastructure, but rather just need to provide the organism under investigation in a convenient format also for non-Biocs. I have not found something similar in existing packages and I am wondering whether this could be something of general interest. Best, Ludwig -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ 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 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] mapIds methods for ExpressionSet and SummarizedExperiment
Dear Bioc Team, I have implemented mapIds methods mapping featureNames (ExpressionSet) and rownames (SummarizedExperiment) between major gene ID types such as ENSEMBL and ENTREZ by passing that on AnnotationDbi::mapIds. Given an ExpressionSet/SummarizedExperiment and an organism under investigation such as 'Homo sapiens', the methods are checking whether the corresponding org.db package is available, otherwise the package is automatically installed and loaded. Subsequently, the featureNames/rownames are mapped from the specified from.id.type to the desired to.id.type, corresponding to keytypes of the org.db package. Options to deal with NA and duplicate mappings are also provided in order to ensure that featureNames/rownames are unique after the mapping. Advantage is that end users do not require knowledge of the Bioc annotation infrastructure, but rather just need to provide the organism under investigation in a convenient format also for non-Biocs. I have not found something similar in existing packages and I am wondering whether this could be something of general interest. Best, Ludwig -- Dipl.-Bioinf. Ludwig Geistlinger Lehr- und Forschungseinheit für Bioinformatik Institut für Informatik Ludwig-Maximilians-Universität München Amalienstrasse 17, 2. Stock, Büro A201 80333 München Tel.: 089-2180-4067 eMail: ludwig.geistlin...@bio.ifi.lmu.de ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
