[GenABEL-dev] using reshuffle

[Yurii Aulchenko]

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]$
>



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