I had used Permutation in Plink to check the validity of my markers after 10000 permutations. I used the command --mperm 10000 for permutation. Is there a way to get the Standard Deviation of the P values using plink or any other tools? I think it is necessary to know the range of P values that were obtained but is it possible to get those?
You can get the p-value from the permutation. But if you want the sd of the p-value, you need replicate the permutation multiple times to see how variable the p-value is. But I doubt there is any big variation since you have 10000 replicates in one permutation.
you can get the probability value quite easily from the permutation. and calculation of SD is very common practice but as you have a large number of replicates I hope that you will get huge variation. My suggestion is that the experiment should be designed in such a way that there should be less replicates.
Isolate your column of p values using the 'cut' command. For example, if your p values are in the fourth column of '1000_permutations.out', type cut -d' ' -f4 1000_permutations.out > p_values.txt'. Open up R, change your working directory to whatever folder houses 'p_values.txt' and type 'results
Thank you Christopher Whelan and Rajesh Gautam.. Thanks for the help..
Actually Hongyan Xu and Satyajit Kanungo.. Am new to this totally as I am a student of Industrial Biotechnology and I couldn't understand what you meant by replicates here?? Sorry if the question is silly..
Rajesh Gautam Sir.. I can use Microsoft Excel to calculate the SD but for that I need to have all the P values, but I have only the P value that I got after 10000 permutations..
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