[GenABEL-dev] using reshuffle

[Yurii Aulchenko]

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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