[GenABEL-dev] using reshuffle

[Содбо Шарапов]

Hello!
I'll will check reshuffle tomorrow.
20.07.2013 22:26 пользователь "Yurii Aulchenko" <yurii.aulchenko at gmail.com>
написал:

> Another point: apparently you do not check boundaries - e.g. when I try to
> get results for trait #200,000 (I have 107,000 only) I get the core dump.
>
> YA
>
> On Sat, Jul 20, 2013 at 5:15 PM, Yurii Aulchenko <
> yurii.aulchenko at gmail.com> wrote:
>
>> Hi Sodbo,
>>
>> It seems that reshuffle does not work correctly, at least I can not get
>> to the results with it (see below). I use a dataset with ~107k traits and
>> ~280k SNPs.
>>
>> Any idea? - do I do something wrong?
>>
>> YA
>>
>> With perl-extractor I get chi2 of 62
>>
>> ya567666 at cluster:~[167]$ perl extractCell.pl /hpcwork/df938257/natgen/B2
>> 329 209602 | gawk '{print $_,($2/$4)^2}'
>>  -0.165153577923775 0.580845952033997 0.0298683661967516
>> 0.0734809562563896 -0.00155110028572381 62.4845
>>
>> But this is not the case with reshuffle (and also I do not get any output
>> with reshuffle /hpcwork/df938257/natgen/B2 --chi=30, while I know there are
>> such chi2's in the results)
>>
>> ya567666 at cluster:~[167]$ reshuffle /hpcwork/df938257/natgen/B2
>> --snps=209602 --traits=329 --chi
>> Finish iout_file read   0.11 sec
>> Start_write_chi_data=0.14 sec
>> End_write_chi_trait     spm_1_AND_spmp_23 0.14 sec
>> Finish_write_chi_data   0.14 sec
>> Finish reshuffling 0.14 sec
>> ya567666 at cluster:~[168]$ cat chi_data.txt
>> SNP     Trait   beta_1  beta_SNP        se_1    se_SNP  cov_SNP_1
>> Chi2
>> rs4902242       spm_1_AND_spmp_23       -0.00234050769358873
>>  -0.0338250175118446     0.128280490636826   0.0329618416726589
>> 0.0770578160881996      1.05306001371466
>> ya567666 at cluster:~[169]$
>>
>
>
>
> --
> -----------------------------------------------------
> Yurii S. Aulchenko
>
> [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter<http://twitter.com/YuriiAulchenko>] [
> Blog <http://yurii-aulchenko.blogspot.nl/> ]
>
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