From lennart at karssen.org Mon Nov 3 10:07:00 2014 From: lennart at karssen.org (L.C. Karssen) Date: Mon, 03 Nov 2014 10:07:00 +0100 Subject: [GenABEL-dev] Review needed for MultiABEL In-Reply-To: References:

Message-ID: <545745B4.6030404@karssen.org> Dear Xia, On 30-10-14 23:12, Xia Shen wrote: > Dear list, > > Thanks Lennart for a fairly good introduction of me! Following this, I > would like to inform you that a new package, MultiABEL, has been > committed to R-Forge and successfully built. This is the first (R-only) > version, which performs multivariate GWA analysis, i.e. testing a group > of (co)related phenotypes against each single variant. There are also a > replication analysis module and a simple meta-analysis module included. > The GWA module is compatible with both GenABEL (directly typed data) and > DatABEL (imputed data) formats of genotypes. Thank you for contributing this package. It looks like a good addition to the GenABEL suite. > > I would kindly ask whether any of you could do a technical review of > this new package, to ensure the coding follows GenABEL standards. You > are certainly also welcome to contribute to future development of this > package. We will be happy to do the review. Any volunteers can reply to the list or send me a private e-mail (although we prefer the 'open' route of using the mailing list). Some time ago we set up a list of suggested questions to aid package reviews at http://genabel.r-forge.r-project.org/packageReviewGuidelines.html (of course, suggestions for additions, corrections, etc. are very welcome). Best regards, Lennart. > > Thanks in advance! > > Xia > > *Xia Shen, PhD* > shen.se > > Department of Medical Epidemiology & Biostatistics > Karolinska Institutet > Nobels v?g 12A > SE-171 77 Stockholm > SWEDEN > > MRC Human Genetics Unit > MRC Institute of Genetics & Molecular Medicine > University of Edinburgh > Western General Hospital > Crewe Road > EH4 2XU Edinburgh > UK > >> >> Date: Thu, 30 Oct 2014 13:34:25 +0100 >> From: "L.C. Karssen" > >> To: GenABEL Development list >> > > >> Subject: [GenABEL-dev] Introducing Xia Shen >> Message-ID: <54523051.4060502 at karssen.org >> > >> Content-Type: text/plain; charset="utf-8" >> >> Dear list, >> >> With this e-mail I'd like to introduce Xia Shen as a "new" member of our >> community. Some of you may know Xia from his contributions to the devel >> list or his work on GenABEL's polygenic_hglm. >> >> In the past, both Yurii and I have worked with Xia in the past and now >> Xia has asked whether he could join the GenABEL project as well. Xia has >> a background in statistical genetics and has already worked on several R >> packages, notably bigRR [1] and hglm [2], which are both in the Suggests >> list of the GenABEL package. >> >> Xia has been working on a new package he'd like to include in the >> GenABEL suite. I'm sure you will here more on that in the near future. >> In order to set up the package Xia has been given commit access to the >> SVN repo. >> >> Xia, I wish you a warm welcome and look forward to your contributions. >> >> Best, >> >> Lennart. >> >> >> [1] http://cran.r-project.org/web/packages/bigRR/index.html >> [2] http://cran.r-project.org/web/packages/hglm/index.html >> -- >> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >> L.C. Karssen >> Utrecht >> The Netherlands >> >> lennart at karssen.org >> http://blog.karssen.org >> GPG key ID: A88F554A >> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- > > > > _______________________________________________ > genabel-devel mailing list > genabel-devel at lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel > -- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* L.C. Karssen Utrecht The Netherlands lennart at karssen.org http://blog.karssen.org GPG key ID: A88F554A -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 213 bytes Desc: OpenPGP digital signature URL: From nicola.pirastu at burlo.trieste.it Mon Nov 3 13:47:44 2014 From: nicola.pirastu at burlo.trieste.it (Pirastu Nicola) Date: Mon, 3 Nov 2014 12:47:44 +0000 Subject: [GenABEL-dev] Review needed for MultiABEL In-Reply-To: <545745B4.6030404@karssen.org> References:

<545745B4.6030404@karssen.org> Message-ID: <0AE61AB8-BF67-4669-A84B-A92089639BEC@burlo.trieste.it> Dear Lennart and Xia, since I?m in a similar situation as Xia (I wold have a package waiting for second review), I would propose to review Xia?s package while he could review mine if he has time. I think this would speed up things. Also I have data which would be very good to test as multi-trait. Anyways I would be happy to review it and test it. Best. Nicola Il giorno 03/nov/2014, alle ore 10:07, L.C. Karssen > ha scritto: Dear Xia, On 30-10-14 23:12, Xia Shen wrote: Dear list, Thanks Lennart for a fairly good introduction of me! Following this, I would like to inform you that a new package, MultiABEL, has been committed to R-Forge and successfully built. This is the first (R-only) version, which performs multivariate GWA analysis, i.e. testing a group of (co)related phenotypes against each single variant. There are also a replication analysis module and a simple meta-analysis module included. The GWA module is compatible with both GenABEL (directly typed data) and DatABEL (imputed data) formats of genotypes. Thank you for contributing this package. It looks like a good addition to the GenABEL suite. I would kindly ask whether any of you could do a technical review of this new package, to ensure the coding follows GenABEL standards. You are certainly also welcome to contribute to future development of this package. We will be happy to do the review. Any volunteers can reply to the list or send me a private e-mail (although we prefer the 'open' route of using the mailing list). Some time ago we set up a list of suggested questions to aid package reviews at http://genabel.r-forge.r-project.org/packageReviewGuidelines.html (of course, suggestions for additions, corrections, etc. are very welcome). Best regards, Lennart. Thanks in advance! Xia *Xia Shen, PhD* shen.se Department of Medical Epidemiology & Biostatistics Karolinska Institutet Nobels v?g 12A SE-171 77 Stockholm SWEDEN MRC Human Genetics Unit MRC Institute of Genetics & Molecular Medicine University of Edinburgh Western General Hospital Crewe Road EH4 2XU Edinburgh UK Date: Thu, 30 Oct 2014 13:34:25 +0100 From: "L.C. Karssen" > To: GenABEL Development list

> Subject: [GenABEL-dev] Introducing Xia Shen Message-ID: <54523051.4060502 at karssen.org > Content-Type: text/plain; charset="utf-8" Dear list, With this e-mail I'd like to introduce Xia Shen as a "new" member of our community. Some of you may know Xia from his contributions to the devel list or his work on GenABEL's polygenic_hglm. In the past, both Yurii and I have worked with Xia in the past and now Xia has asked whether he could join the GenABEL project as well. Xia has a background in statistical genetics and has already worked on several R packages, notably bigRR [1] and hglm [2], which are both in the Suggests list of the GenABEL package. Xia has been working on a new package he'd like to include in the GenABEL suite. I'm sure you will here more on that in the near future. In order to set up the package Xia has been given commit access to the SVN repo. Xia, I wish you a warm welcome and look forward to your contributions. Best, Lennart. [1] http://cran.r-project.org/web/packages/bigRR/index.html [2] http://cran.r-project.org/web/packages/hglm/index.html -- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* L.C. Karssen Utrecht The Netherlands lennart at karssen.org http://blog.karssen.org GPG key ID: A88F554A -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- _______________________________________________ genabel-devel mailing list genabel-devel at lists.r-forge.r-project.org https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel -- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* L.C. Karssen Utrecht The Netherlands lennart at karssen.org http://blog.karssen.org GPG key ID: A88F554A -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- _______________________________________________ genabel-devel mailing list genabel-devel at lists.r-forge.r-project.org https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel AVVISO DI RISERVATEZZA Informazioni riservate possono essere contenute nel messaggio o nei suoi allegati. Se non siete i destinatari indicati nel messaggio, o responsabili per la sua consegna alla persona, o se avete ricevuto il messaggio per errore, siete pregati di non trascriverlo, copiarlo o inviarlo a nessuno. In tal caso vi invitiamo a cancellare il messaggio ed i suoi allegati. Grazie. CONFIDENTIALITY NOTICE Confidential information may be contained in this message or in its attachments. If you are not the addressee indicated in this message, or responsible for message delivering to that person, or if you have received this message in error, you may not transcribe, copy or deliver this message to anyone. In that case, you should delete this message and its attachments. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: From shenxia911 at gmail.com Tue Nov 4 14:47:39 2014 From: shenxia911 at gmail.com (Xia Shen) Date: Tue, 4 Nov 2014 13:47:39 +0000 Subject: [GenABEL-dev] Review needed for MultiABEL In-Reply-To: References: Message-ID: <6BE6A04C-540B-4B2C-87F8-181C387B09CF@gmail.com> Hi Nicola, Thanks for being willing to review my package. I certainly can help review yours if I have time. Which package is the one that you are waiting for review? You said ?second? - did you have a first review already? Xia > Date: Mon, 3 Nov 2014 12:47:44 +0000 > From: Pirastu Nicola > To: "L.C. Karssen" > Cc: "genabel-devel at lists.r-forge.r-project.org" > > Subject: Re: [GenABEL-dev] Review needed for MultiABEL > Message-ID: <0AE61AB8-BF67-4669-A84B-A92089639BEC at burlo.trieste.it> > Content-Type: text/plain; charset="windows-1252" > > Dear Lennart and Xia, > > since I?m in a similar situation as Xia (I wold have a package waiting for second review), > > I would propose to review Xia?s package while he could review mine if he has time. > > I think this would speed up things. Also I have data which would be very good to test as multi-trait. > > Anyways I would be happy to review it and test it. > > Best. > > Nicola > > > Il giorno 03/nov/2014, alle ore 10:07, L.C. Karssen > ha scritto: > > Dear Xia, > > On 30-10-14 23:12, Xia Shen wrote: > Dear list, > > Thanks Lennart for a fairly good introduction of me! Following this, I > would like to inform you that a new package, MultiABEL, has been > committed to R-Forge and successfully built. This is the first (R-only) > version, which performs multivariate GWA analysis, i.e. testing a group > of (co)related phenotypes against each single variant. There are also a > replication analysis module and a simple meta-analysis module included. > The GWA module is compatible with both GenABEL (directly typed data) and > DatABEL (imputed data) formats of genotypes. > > Thank you for contributing this package. It looks like a good addition > to the GenABEL suite. > > > I would kindly ask whether any of you could do a technical review of > this new package, to ensure the coding follows GenABEL standards. You > are certainly also welcome to contribute to future development of this > package. > > We will be happy to do the review. Any volunteers can reply to the list > or send me a private e-mail (although we prefer the 'open' route of > using the mailing list). > Some time ago we set up a list of suggested questions to aid package > reviews at > http://genabel.r-forge.r-project.org/packageReviewGuidelines.html (of > course, suggestions for additions, corrections, etc. are very welcome). > > > Best regards, > > Lennart. > > > Thanks in advance! > > Xia > > *Xia Shen, PhD* > shen.se > > Department of Medical Epidemiology & Biostatistics > Karolinska Institutet > Nobels v?g 12A > SE-171 77 Stockholm > SWEDEN > > MRC Human Genetics Unit > MRC Institute of Genetics & Molecular Medicine > University of Edinburgh > Western General Hospital > Crewe Road > EH4 2XU Edinburgh > UK > > > Date: Thu, 30 Oct 2014 13:34:25 +0100 > From: "L.C. Karssen" > > To: GenABEL Development list > > > > Subject: [GenABEL-dev] Introducing Xia Shen > Message-ID: <54523051.4060502 at karssen.org > > > Content-Type: text/plain; charset="utf-8" > > Dear list, > > With this e-mail I'd like to introduce Xia Shen as a "new" member of our > community. Some of you may know Xia from his contributions to the devel > list or his work on GenABEL's polygenic_hglm. > > In the past, both Yurii and I have worked with Xia in the past and now > Xia has asked whether he could join the GenABEL project as well. Xia has > a background in statistical genetics and has already worked on several R > packages, notably bigRR [1] and hglm [2], which are both in the Suggests > list of the GenABEL package. > > Xia has been working on a new package he'd like to include in the > GenABEL suite. I'm sure you will here more on that in the near future. > In order to set up the package Xia has been given commit access to the > SVN repo. > > Xia, I wish you a warm welcome and look forward to your contributions. > > Best, > > Lennart. > > > [1] http://cran.r-project.org/web/packages/bigRR/index.html > [2] http://cran.r-project.org/web/packages/hglm/index.html > -- > *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* > L.C. Karssen > Utrecht > The Netherlands > > lennart at karssen.org > http://blog.karssen.org > GPG key ID: A88F554A > -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- > > > > _______________________________________________ > genabel-devel mailing list > genabel-devel at lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel > > > -- > *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* > L.C. Karssen > Utrecht > The Netherlands > > lennart at karssen.org > http://blog.karssen.org > GPG key ID: A88F554A > -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- > > _______________________________________________ > genabel-devel mailing list > genabel-devel at lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel > > AVVISO DI RISERVATEZZA Informazioni riservate possono essere contenute nel messaggio o nei suoi allegati. Se non siete i destinatari indicati nel messaggio, o responsabili per la sua consegna alla persona, o se avete ricevuto il messaggio per errore, siete pregati di non trascriverlo, copiarlo o inviarlo a nessuno. In tal caso vi invitiamo a cancellare il messaggio ed i suoi allegati. Grazie. CONFIDENTIALITY NOTICE Confidential information may be contained in this message or in its attachments. If you are not the addressee indicated in this message, or responsible for message delivering to that person, or if you have received this message in error, you may not transcribe, copy or deliver this message to anyone. In that case, you should delete this message and its attachments. Thank you. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > ------------------------------ > > _______________________________________________ > genabel-devel mailing list > genabel-devel at lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel > > End of genabel-devel Digest, Vol 48, Issue 3 > ******************************************** From lennart at karssen.org Wed Nov 26 14:02:53 2014 From: lennart at karssen.org (L.C. Karssen) Date: Wed, 26 Nov 2014 14:02:53 +0100 Subject: [GenABEL-dev] [Genabel-commits] r1892 - pkg/MultiABEL/R In-Reply-To: <20141126055102.4864A187831@r-forge.r-project.org> References: <20141126055102.4864A187831@r-forge.r-project.org> Message-ID: <5475CF7D.3000009@karssen.org> Hi Xia, Thanks for the update to MultiABEL. If I remember correctly, this is the first time I do a commit review for you. In the GenABEL project we try to do quick reviews of all code that is committed. In the review we look both at coding style and at the effect of the code (Does it do what it is supposed to do? Are there any side effects? Etc.). Feel free to help out by subscribing to the GenABEL commit mailing list (if you haven't already done so). Please find my comments below. On 26-11-14 06:51, noreply at r-forge.r-project.org wrote: > Author: shenxia > Date: 2014-11-26 06:51:01 +0100 (Wed, 26 Nov 2014) > New Revision: 1892 > > Modified: > pkg/MultiABEL/R/Multivariate.R > Log: Next time, could you please add a log message to your commit? The idea of the log message is that it briefly explains what the change does/is supposed to do, which bug is fixed, which (partial) feature added, etc. > > > Modified: pkg/MultiABEL/R/Multivariate.R > =================================================================== > --- pkg/MultiABEL/R/Multivariate.R 2014-11-18 12:13:25 UTC (rev 1891) > +++ pkg/MultiABEL/R/Multivariate.R 2014-11-26 05:51:01 UTC (rev 1892) > @@ -68,7 +68,7 @@ > GenABEL <- FALSE > cat(' OK\n') > } else if (!is.null(gwaa.data)) { > - pheno <- gwaa.data at phdata > + if (!is.null(phenofile)) pheno <- read.table(phenofile, header = TRUE) else pheno <- gwaa.data at phdata The line above is rather long. This doesn't help making the code easily readable. Moreover, since it is an if clause it is better to add {}s to make it 100% clear what is supposed to be in the if and else parts. For this statement the intention is quite clear, but imagine someone adds a debug print statement somewhere, or wants to quickly add something in the if statement. Having the curly braces is good practice (and part of our coding standards). Thanks again for your time and efforts, Lennart. > GenABEL <- TRUE > cat(' OK\n') > } else { > > _______________________________________________ > Genabel-commits mailing list > Genabel-commits at lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-commits > -- *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* L.C. Karssen Utrecht The Netherlands lennart at karssen.org http://blog.karssen.org GPG key ID: A88F554A -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 213 bytes Desc: OpenPGP digital signature URL: From yurii.aulchenko at gmail.com Wed Nov 26 14:27:15 2014 From: yurii.aulchenko at gmail.com (Yurii Aulchenko) Date: Wed, 26 Nov 2014 14:27:15 +0100 Subject: [GenABEL-dev] [Genabel-commits] r1892 - pkg/MultiABEL/R In-Reply-To: <5475CF7D.3000009@karssen.org> References: <20141126055102.4864A187831@r-forge.r-project.org> <5475CF7D.3000009@karssen.org> Message-ID: <2733C5F5-D86E-4279-9D77-6B065FD12911@gmail.com> one comment below > On Nov 26, 2014, at 14:02 PM, L.C. Karssen wrote: > > Hi Xia, > > Thanks for the update to MultiABEL. If I remember correctly, this is the > first time I do a commit review for you. > In the GenABEL project we try to do quick reviews of all code that is > committed. In the review we look both at coding style and at the effect > of the code (Does it do what it is supposed to do? Are there any side > effects? Etc.). > Feel free to help out by subscribing to the GenABEL commit mailing list > (if you haven't already done so). > > Please find my comments below. > > On 26-11-14 06:51, noreply at r-forge.r-project.org wrote: >> Author: shenxia >> Date: 2014-11-26 06:51:01 +0100 (Wed, 26 Nov 2014) >> New Revision: 1892 >> >> Modified: >> pkg/MultiABEL/R/Multivariate.R >> Log: > > Next time, could you please add a log message to your commit? The idea > of the log message is that it briefly explains what the change does/is > supposed to do, which bug is fixed, which (partial) feature added, etc. > >> >> >> Modified: pkg/MultiABEL/R/Multivariate.R >> =================================================================== >> --- pkg/MultiABEL/R/Multivariate.R 2014-11-18 12:13:25 UTC (rev 1891) >> +++ pkg/MultiABEL/R/Multivariate.R 2014-11-26 05:51:01 UTC (rev 1892) >> @@ -68,7 +68,7 @@ >> GenABEL <- FALSE >> cat(' OK\n') >> } else if (!is.null(gwaa.data)) { >> - pheno <- gwaa.data at phdata >> + if (!is.null(phenofile)) pheno <- read.table(phenofile, header = TRUE) else pheno <- gwaa.data at phdata Better use phdata(object) method than direct access to slot. This should make your code more stable to potential changes in underlying class in the future. best, Yurii > > The line above is rather long. This doesn't help making the code easily > readable. Moreover, since it is an if clause it is better to add {}s to > make it 100% clear what is supposed to be in the if and else parts. For > this statement the intention is quite clear, but imagine someone adds a > debug print statement somewhere, or wants to quickly add something in > the if statement. Having the curly braces is good practice (and part of > our coding standards). > > > Thanks again for your time and efforts, > > Lennart. > >> GenABEL <- TRUE >> cat(' OK\n') >> } else { >> >> _______________________________________________ >> Genabel-commits mailing list >> Genabel-commits at lists.r-forge.r-project.org >> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-commits >> > > -- > *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* > L.C. Karssen > Utrecht > The Netherlands > > lennart at karssen.org > http://blog.karssen.org > GPG key ID: A88F554A > -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- > > _______________________________________________ > genabel-devel mailing list > genabel-devel at lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel