[GenABEL-dev] Suggested change of default weight in GenABEL/ibs()

[Yurii Aulchenko]

I am voting for option 2; as for the version number - no strong opinion.

Xia, would you be willing to summarize this discussion as a feature
request, or to provide a patch?

Best wishes,
Yurii

----------------------
Yurii Aulchenko
(sent from mobile device)

> On Mar 3, 2014, at 4:12 PM, "L.C. Karssen" <lennart at karssen.org> wrote:
>
> Dear all,
>
>> On 28-02-14 14:15, Yurii Aulchenko wrote:
>> In principle I agree this is good idea, rarely "no" (default) option is
>> used; but I am always worried to change defaults as this may destroy
>> people pipelines.
>
> How about issuing a warning? I see two options:
> 1) Keep the current default and issue a warning when the user doesn't
> specify a weight.
> 2) Change the default and when ibs() is run and the weight argument is
> not equal to 'freq', issue a warning saying that the default has changed
> to freq.
>
> Although I haven't used ibs() a lot, I think option 2 is best as it sets
> a sane default.
>
> Another thing to think about: when changing defaults, what do we do with
> the version number. If we only change the minor number (the 8 in 1.8-0),
> people will think not much has changed and this change in default
> behaviour may go unnoticed.
>
>
> Lennart.
>
>>
>> We need third opinion :)
>>
>> Best,
>> Y
>>
>> ----------------------
>> Yurii Aulchenko
>> (sent from mobile device)
>>
>> On Feb 28, 2014, at 3:45 PM, Xia Shen <shenxia911 at gmail.com
>> <mailto:shenxia911 at gmail.com>> wrote:
>>
>>> Hi,
>>>
>>> I suggest to change the default weight argument in the GenABEL/ibs()
>>> function to be set to "freq" instead of "no". I have colleagues
>>> constantly forget to set to "freq" and produce, what I would call,
>>> "wrong" kinship matrix.
>>>
>>> *Xia Shen*
>>> PhD
>>>
>>> Division of Computational Genetics
>>> Department of Clinical Science
>>> *Swedish University of Agricultural Sciences*
>>> Uppsala, Sweden
>>>
>>> www.shen.se <http://www.shen.se>
>>>
>>>
>>>
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>>
>>
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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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