From k.zhong at erasmusmc.nl Thu Feb 19 14:27:22 2015 From: k.zhong at erasmusmc.nl (K. Zhong) Date: Thu, 19 Feb 2015 13:27:22 +0000 Subject: [GenABEL-dev] Proposing the CollapsABEL R package for inclusion Message-ID: Dear all, I have recently finished an R package for compound heterozygosity analysis for microarray/NGS data. This package (named CollapsABEL) implements an extended version of the CDH test (see DOI: 10.1371/journal.pone.0028145) in a flexible, efficient and user friendly way and has already proved useful for our analysis with certain dermatology traits. CDH test has been implemented before as a function in the GenABEL package, but due to the simplicity of the method itself and restriction from the data format it uses, it is practically not very useful. CollapsABEL overcomes these limitations and provides a nice streamlined solution in your hands, for which reason I think it would be a nice addition to the GenABEL family. The project is hosted on bitbucket: https://bitbucket.org/kindlychung/collapsabel/overview The R manual and an extensive tutorial can be found here: https://bitbucket.org/kindlychung/collapsabel/downloads If you are willing to review this package, please let me know. Best regards, Kaiyin ZHONG ------------------ FMB, Erasmus MC kaiyin.co.vu k.zhong at erasmusmc.nl kindlychung at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From lennart at karssen.org Sun Feb 22 22:16:42 2015 From: lennart at karssen.org (L.C. Karssen) Date: Sun, 22 Feb 2015 22:16:42 +0100 Subject: [GenABEL-dev] Proposing the CollapsABEL R package for inclusion In-Reply-To: References: Message-ID: <54EA473A.8040104@karssen.org> Dear Kaiyin, Thank you for your willingness to contribute to the GenABEL project. On 19-02-15 14:27, K. Zhong wrote: > Dear all, > > I have recently finished an R package for compound heterozygosity > analysis for microarray/NGS data. This package (named CollapsABEL) > implements an extended version of the CDH test > (see > DOI: 10.1371/journal.pone.0028145) in a flexible, efficient and user > friendly way and has already proved useful for our analysis with > certain dermatology traits. That sounds interesting indeed! To me it sounds like a useful addition to the GenABEL suite. > CDH test has been implemented before as a > function in the GenABEL package, but due to the simplicity of the method > itself and restriction from the data format it uses, it is practically > not very useful. CollapsABEL overcomes these limitations and provides a > nice streamlined solution in your hands, for which reason I think it > would be a nice addition to the GenABEL family. Do you have a suggestion on what to do with the current CDH test in the GenABEL package? Is it worth to spend time maintaining it, or should we replace it with a message pointing people to CollapsABEL (of course assuming CollapsABEL gets accepted into the GenaBEL suite)? > > The project is hosted on > bitbucket: https://bitbucket.org/kindlychung/collapsabel/overview > The R manual and an extensive tutorial can be found here: > https://bitbucket.org/kindlychung/collapsabel/downloads Thank you for providing these links. > > If you are willing to review this package, please let me know. I hope someone will step forward to do this. If you don't get a reaction in the coming few weeks, please feel free to send a reminder to the list. Best regards, Lennart Karssen. > > > Best regards, > > Kaiyin ZHONG > ------------------ > FMB, Erasmus MC > kaiyin.co.vu > k.zhong at erasmusmc.nl > kindlychung at gmail.com > > > > > > _______________________________________________ > 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 k.zhong at erasmusmc.nl Mon Feb 23 14:42:19 2015 From: k.zhong at erasmusmc.nl (K. Zhong) Date: Mon, 23 Feb 2015 13:42:19 +0000 Subject: [GenABEL-dev] Proposing the CollapsABEL R package for inclusion In-Reply-To: <54EA473A.8040104@karssen.org> References: <54EA473A.8040104@karssen.org> Message-ID: Dear Lennart, At the moment I think it would be nice to keep the function as it is for current users of it and show them a message about the new package. Thank you for bringing this up. Best regards, Kaiyin ZHONG ------------------ FMB, Erasmus MC kaiyin.co.vu k.zhong at erasmusmc.nl kindlychung at gmail.com On 22/02/15 22:16, "L.C. Karssen" wrote: >Dear Kaiyin, > >Thank you for your willingness to contribute to the GenABEL project. > >On 19-02-15 14:27, K. Zhong wrote: >> Dear all, >> >> I have recently finished an R package for compound heterozygosity >> analysis for microarray/NGS data. This package (named CollapsABEL) >> implements an extended version of the CDH test >> >>>> (see >> DOI: 10.1371/journal.pone.0028145) in a flexible, efficient and user >> friendly way and has already proved useful for our analysis with >> certain dermatology traits. > >That sounds interesting indeed! To me it sounds like a useful addition >to the GenABEL suite. > >> CDH test has been implemented before as a >> function in the GenABEL package, but due to the simplicity of the method >> itself and restriction from the data format it uses, it is practically >> not very useful. CollapsABEL overcomes these limitations and provides a >> nice streamlined solution in your hands, for which reason I think it >> would be a nice addition to the GenABEL family. > >Do you have a suggestion on what to do with the current CDH test in the >GenABEL package? Is it worth to spend time maintaining it, or should we >replace it with a message pointing people to CollapsABEL (of course >assuming CollapsABEL gets accepted into the GenaBEL suite)? > >> >> The project is hosted on >> bitbucket: https://bitbucket.org/kindlychung/collapsabel/overview >> The R manual and an extensive tutorial can be found here: >> https://bitbucket.org/kindlychung/collapsabel/downloads > >Thank you for providing these links. > >> >> If you are willing to review this package, please let me know. > >I hope someone will step forward to do this. If you don't get a reaction >in the coming few weeks, please feel free to send a reminder to the list. > > >Best regards, > >Lennart Karssen. > >> >> >> Best regards, >> >> Kaiyin ZHONG >> ------------------ >> FMB, Erasmus MC >> kaiyin.co.vu >> k.zhong at erasmusmc.nl >> kindlychung at gmail.com >> >> >> >> >> >> _______________________________________________ >> 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-deve >>l >> > >-- >*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* >L.C. Karssen >Utrecht >The Netherlands > >lennart at karssen.org >http://blog.karssen.org >GPG key ID: A88F554A >-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- >