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Detecting epistasis via Markov bases

(co-authored with Anna-Sapfo Malaspinas)

Research paper:

Our paper "Detecting epistasis via Markov bases" can be found here. 


Markov bases:

  • The Markov basis for the no 3-way interaction model consists of 15 moves and can be found here.

  • The Markov basis for the multiplicative model on two SNPs consists of 49 moves and can be found here.

  • The Markov basis for the additive model on two SNPs consists of 156 moves and can be found here.


Note: The Markov bases are in R format and the cell entries of the corresponding 3x3x2 tables are reported as vectors in the following order:
(n111, n211 , n311, n121, n221, n321, n131, n231, n331, n112, n212 , n312, n122, n222, n322, n132, n232, n332)

Code:

The code for using the extended version of Fisher's exact test for detecting epistasis can be found here. It runs in R. The code uses the Markov basis of the no 3-way interaction model given above. It also takes as input a file named ListOfTables.RDATA consisting of the  3x3x2 data tables. In ListOfTables.RDATA  there are 10 chose 2 tables corresponding to all possible pairs of SNPs among the 10 SNPs with the lowest marginal p-values. The program outputs a table called out consisting of the chi-square statistic of the given data table, its p-value before Bonferroni correction, and the value 1 for significant and 0 for not significant using a 5% cutoff after Bonferroni correction.