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

[L.C. Karssen]

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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> 

-- 
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L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

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