Reference no: EM133234734

Fisher's Exact Test

In this scenario, you can represent the data as contingency tables and the effect sizes as odds ratios (please refer to the walk through lecture and slides). For each SNP, if there is significant evidence that the odds ratio for allele C is higher than 1, you can conclude that allele C is among the causes of the complex genetic trait.

The Fisher's exact test is a statistical test performed on the contingency tables and tests whether the odds ratio of the underlying populations are close to 1 or not. Using the scipy's fisher exact function, find the p-value associatedw ith each SNP for your data set. Assuming an effective p-value of 5 × 10-8, which SNPs can be considered statistically significant regarding the complex genetic trait? Based on the documentation of fisher exact function, you need to explain what the null hypothesis of this test is and what it means. Also you need to choose to explain how you choose the alternative argument int his function. You have to provide a file named results.csv containing the p-values for each SNP in the first column and the SNPs that are significant in the second column. You should also report the number of significant SNPs in your written answer.