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

[K. Zhong]

Dear all,

I have read through the technical review guidelines and I think
CollapsABEL satisfies all requirements except that `R CMD check` and `R
CMD check -as-cran` both produces one warning and two notes. The warning
is about my .git folder, which is for version control, and won¹t be
present once a binary package is built, so this is a non-issue. The notes
are about some ³global variable² that are not global at all, and this is a
known bug of `R CMD check` (see http://tinyurl.com/o9p6vxf for an
example). 

So could anyone please review this package? The submission of our paper is
waiting on this. Thanks!


Best regards,
Kaiyin ZHONG
------------------
FMB, Erasmus MC
kaiyin.co.vu <http://kaiyin.co.vu>
k.zhong at erasmusmc.nl
kindlychung at gmail.com








On 23/02/15 14:42, "K. Zhong" <k.zhong at erasmusmc.nl> wrote:

>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.002814
>>>5
>>>> (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>
>>> 
>>> 
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> 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-dev
>>>e
>>>l
>>> 
>>
>>-- 
>>*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>>L.C. Karssen
>>Utrecht
>>The Netherlands
>>
>>lennart at karssen.org
>>http://blog.karssen.org
>>GPG key ID: A88F554A
>>-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>>
>