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plink epistasis result

Hi!

I tried to make network using plink --fast-epistasis results.

But result has only one unique SNP-SNP interaction.

For example SNP_A ,SNP_B has interaction using plink but SNP_A and another interaction doesn't exist.

Is there any way to get all possible interactions?

Please help me.

Thank you so much!

snp
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written by 496527 • 496527

If you post your log here that would help. It could be because, by default, PLINK will only output SNP x SNP interactions which pass a given p-value threshold, which is controlled with the --epi1 flag. Does setting '--epi1 1' work?

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written by mbyvcm mbyvcm

1 answer

Thank you so much your comment!

My log is here and I actually used --epi1 flag.

Options in effect: --allow-extra-chr --bfile BipolarfinalCC --epi1 0.05 --fast-epistasis

Hostname: ADMIN1 Working directory: C:\Users\Administrator\Desktop\tplink_format\results_Bipolar Start time: Wed Feb 01 22:44:37 2017

Random number seed: 1485956677 32688 MB RAM detected; reserving 16344 MB for main workspace. 107526 variants loaded from .bim file. 4806 people (2143 males, 2663 females) loaded from .fam. 4806 phenotype values loaded from .fam. Using up to 8 threads (change this with --threads). Before main variant filters, 4806 founders and 0 nonfounders present. Calculating allele frequencies... done. Warning: 2703 het. haploid genotypes present (see plink.hh ); many commands treat these as missing. 107526 variants and 4806 people pass filters and QC. Among remaining phenotypes, 1868 are cases and 2938 are controls. --fast-epistasis: Skipping 2486 monomorphic/non-autosomal sites. --fast-epistasis to plink.epi.cc ... done. 5516648280 valid tests performed, summary written to plink.epi.cc.summary .

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written by 496527 • 496527

you used --epi1 0.05. What happens with --epi1 1?

If you use 0.05 threshold, then your output file we be missing all pairwise interactions that do not report a p-value <=0.05.

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written by mbyvcm mbyvcm

I tried --epi1 1 command but It failed.

So I also tried --fast-epistasis nop command this result is same as epi1 0.05

Thank you!

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written by 496527 • 496527

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