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

Fri May 22 17:05:31 CEST 2015

Dear Lennart,

Thanks a lot for your detailed review, I find it very helpful!
Issues mentioned therein will be fixed as soon as possible.

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

On 22/05/15 16:52, "L.C. Karssen" <lennart at karssen.org> wrote:

>Dear Kaiyin,
>
>Please find attached my review of the CollapsABEL package. All in all I
>must say the package is well-written and I would be happy to include it
>in the GenABEL suite once the issues mentioned in the review have been
>dealt with.
>
>
>With my apologies for the delay in the review process.
>Best regards,
>
>Lennart Karssen.
>
>On 16-04-15 15:09, L.C. Karssen wrote:
>> Dear Kaiyin,
>> 
>> A quick update on the package review: I'm having some troubles with my R
>> development environment. I hope to resolve them today so that I can
>> continue with my review of your package.
>> 
>> 
>> Lennart.
>> 
>> On 14-04-15 11:24, L.C. Karssen wrote:
>>> Dear Kaiyin,
>>>
>>>
>>> On 13-04-15 10:05, K. Zhong wrote:
>>>> Dear all,
>>>>
>>>> I have read through the technical review guidelines
>>>
>>> Thank you for that. Also thanks for bringing CollapsABEL back to our
>>> attention, unfortunately it fell of my radar.
>>>
>>>> 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.
>>>
>>> I agree.
>>>
>>>> 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). 
>>>
>>> Aha. This is more reason for concern. From my own experience the CRAN
>>> staff is quite strickt. Thanks for looking into "prior art". Since the
>>> SE post you refer to is three years old and the GranovaGG package it
>>> relates to is now in CRAN, I agree that we should see if it gets
>>> accepted. However, be prepared to act in case of comments from CRAN.
>>>
>>>>
>>>> So could anyone please review this package? The submission of our
>>>>paper is
>>>> waiting on this. Thanks!
>>>
>>> I will review the package today. I will also try to contact other
>>> potential reviewers directly.
>>>
>>>
>>> Best regards,
>>>
>>> Lennart.
>>>
>>>>
>>>>
>>>> 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.00
>>>>>>>2814
>>>>>>> 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>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
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>>>>>>> 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
>>>>>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>>>>>>
>>>>>
>>>>
>>>
>>>
>>>
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>> 
>> 
>> 
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>>l
>> 
>
>-- 
>*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>L.C. Karssen
>Utrecht
>The Netherlands
>
>lennart at karssen.org
>http://blog.karssen.org
>GPG key ID: A88F554A
>-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-