Caroline Uhler

 

 

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Software: Detecting epistasis via Markov bases


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, n331n112, 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 calleout 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. 

We simulated 50 association studies under three models of interaction (control, additive and multiplicative) and for three minor allele frequencies (MAF = 0.1, MAF = 0.25 and MAF = 0.4) using HapSample. The 10 chose 2 tables corresponding to all possible pairs of SNPs among the 10 SNPs with the lowest marginal p-values can be found in the files below.

- For the control model: ListOfTables_control_MAF01.zip,  ListOfTables_control_MAF025.zipListOfTables_control_MAF04.zip

- For the additive model: ListOfTables_additive_MAF01.zip, ListOfTables_additive_MAF025.zipListOfTables_additive_MAF04.zip

- For the multiplicative model: ListOfTables_multiplicative_MAF01.zip
ListOfTables_additive_MAF025.zipListOfTables_multiplicative_MAF04.zip

The true causative SNPs for each minor allele frequency are given in the following document:
Causative_SNPS.txt

and the 3x3x2 contingency tables for the causative SNPs can be found in the following files for all three models and all three MAFs under consideration.

- For the control model: CausativeTable_control_MAF01.zip, CausativeTable_control_MAF025.zip, CausativeTable_control_MAF04.zip

- For the additive model: CausativeTable_additive_MAF01.zip, CausativeTable_additive_MAF025.zip, CausativeTable_additive_MAF04.zip

- For the multiplicative model: CausativeTable_multiplicative_MAF01.zip, CausativeTable_multiplicative_MAF025.zip, CausativeTable_multiplicative_MAF04.zip