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

Fri May 22 17:38:27 CEST 2015

Dear Fan,

On 22-05-15 17:03, F. Liu wrote:
> Dear Lennart,
> Thanks so much for your effort! Highly appreciated!

You are welcome!

> Given your contribution, we would like to invite you as an coauthor on this paper. Please let us know if you agree.
> The manuscript is still under preparation, we will let you know when it's ready for coauthors.

Thank you for the offer, I happily accept.

> For now please keep it unseen by public and we shall coordinate its publication time together with the paper.

Of course. No problem.
One important thing to note: if you want to keep the paper "closed" for
now, please remove the GenABEL development mailing list from CC. The
devel list is public and it's archives are published on the web.

Best regards,

Lennart.

> Cheers,
> Fan
> 
> 
> -----Original Message-----
> From: L.C. Karssen [mailto:lennart at karssen.org] 
> Sent: Friday, May 22, 2015 4:53 PM
> To: genabel-devel at lists.r-forge.r-project.org; K. Zhong
> Cc: F. Liu
> Subject: Re: [GenABEL-dev] Proposing the CollapsABEL R package for inclusion
> 
> 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
>>>>>>> .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/gena
>>>>>>> bel-dev
>>>>>>> e
>>>>>>> l
>>>>>>>
>>>>>>
>>>>>> --
>>>>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
>>>>>> 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
>>>
>>
>>
>>
>> _______________________________________________
>> 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-d
>> evel
>>
> 
> --
> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
> L.C. Karssen
> Utrecht
> The Netherlands
> 
> lennart at karssen.org
> http://blog.karssen.org
> GPG key ID: A88F554A
> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
> 

-- 
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
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: <http://lists.r-forge.r-project.org/pipermail/genabel-devel/attachments/20150522/c244a30c/attachment.sig>