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!
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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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?