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Format Chen/diff statistics in columns #20

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alexlancaster opened this issue Jul 13, 2017 · 0 comments
Open

Format Chen/diff statistics in columns #20

alexlancaster opened this issue Jul 13, 2017 · 0 comments
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@alexlancaster
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originally filed by @sjmack on #19

The Chen/Diff test results currently look like this:

3.3. Guo and Thompson HardyWeinberg output (mcmc) [DQB1]
--------------------------------------------------------
Total steps in MCMC: 1000000
Dememorization steps: 2000
Number of Markov chain samples: 1000
Markov chain sample size: 1000
Std. error:       0
p-value (overall): 0.0000*****

Individual genotype p-values found to be significant
Genotype (observed/expected) [Chen's pval] [diff pval]
03:02:12+03:02:12 (18/8.818363) 0.0037** 0.0037**
05:03:01:01+03:02:12 (0/18.105788) 0.0001**** 0.0000*****
05:03:01:01+05:03:01:01 (39/9.293663) 0.0000***** 0.0000*****
06:02:01+05:03:01:01 (0/23.499002) 0.0000***** 0.0000*****
06:02:01+06:02:01 (27/14.854291) 0.0000***** 0.0000*****
06:03:01+04:02:01 (8/0.287425) 0.0000***** 0.0000*****
06:05:01+05:03:01:01 (0/18.105788) 0.0000***** 0.0000*****
06:05:01+06:05:01 (18/8.818363) 0.0019** 0.0019**


3.4. Guo and Thompson HardyWeinberg output (monte-carlo) [DQB1]
---------------------------------------------------------------
Steps in Monte-Carlo randomization: 100000
p-value (overall): 0.0000*****

Individual genotype p-values found to be significant
Genotype (observed/expected) [Chen's pval] [diff pval]
03:02:12+03:02:12 (18/8.818363) 0.0017** 0.0017**
05:03:01:01+03:02:12 (0/18.105788) 0.0000***** 0.0000*****
05:03:01:01+05:03:01:01 (39/9.293663) 0.0000***** 0.0000*****
06:02:01+05:03:01:01 (0/23.499002) 0.0000***** 0.0000*****
06:02:01+06:02:01 (27/14.854291) 0.0007*** 0.0007***
06:03:01+04:02:01 (8/0.287425) 0.0000***** 0.0000*****
06:05:01+05:03:01:01 (0/18.105788) 0.0000**** 0.0000****
06:05:01+06:05:01 (18/8.818363) 0.0016** 0.0016**

Although these Chen/diff results would be easier to read if they were structured more like the other HW results:

03:02:12+03:02:12       (18/8.818363) 0.0037**    0.0037**
05:03:01:01+03:02:12    (0/18.105788) 0.0001****  0.0000*****
05:03:01:01+05:03:01:01 (39/9.293663) 0.0000***** 0.0000*****

However, this latter would be a "nice to have".

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