We showed how to calculate a Chi-square test from a table. Here we will show how to generate the table from data which is in the form of a dataframe, so that you can then perform an association test to see if two columns have an enrichment (or depletion) of shared occurrences.

Download the https://studio.edx.org/c4x/HarvardX/PH525.1x/asset/assoctest.csv file into your R working directory, and then read it into R: d = read.csv("assoctest.csv")

  1. This dataframe reflects the allele status (either AA/Aa or aa) and the case/control status for 72 individuals. Compute the Chi-square test for the association of genotype with case/control status (using the table function and the chisq.test function). Examine the table to see if there appears to be an association. What is the X-squared statistic?

  2. Compute Fisher’s exact test fisher.test for the same table. What is the p-value?