[GenABEL-dev] Proposing the CollapsABEL R package for inclusion

[K. Zhong]

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 <http://kaiyin.co.vu>
k.zhong at erasmusmc.nl
kindlychung at gmail.com








On 22/02/15 22:16, "L.C. Karssen" <lennart at karssen.org> 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
>> 
>><http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0028145
>>> (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 <http://kaiyin.co.vu>
>> k.zhong at erasmusmc.nl <mailto:k.zhong at erasmusmc.nl>
>> kindlychung at gmail.com <mailto:kindlychung at gmail.com>
>> 
>> 
>> 
>> 
>> 
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>> 
>>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
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>