For loop for Multiple Trend in Proportions

When you have only one parameter to test, following my previous tutorial for test for trends in proportions will be sufficient. However, if you have many independent variables to be tested across several dependent variables, it may become quite tedious to do them all one by one. Therefore, I wrote a for-loop that will create all the summary-tables, perform the test for trends in proportions for each table, add the test result to the count matrix and save the output neatly in a csv/excel format. Here I explain each step in the process.

Test for trend in proportions

The test for trends in proportions is also known as the Cochran Armitage test. It performs Chi-squared test for trend in proportions and is used to test whether there is a difference between groups considering the size of the groups. It takes count data from contingency tables where you have one nominal variable with two levels (i.e “Mutated”, “Wild-type”) and the other variable is an ordinal value with minimum 3 values where the variables is naturally ranked

Chi-square in R

The Chi-square test is used to compare differences between two or more categorical variables. All variables must be ordinal or nominal and summarized as a frequency table. It is a non-parametric test, meaning that it is suitable also for data that is not normally distributed. Some of the assumptions for performing a Chi-square test are: Each observation is independent of all the others (one observation per subject), and the categories must be mutually exclusive so that a subject fits into only one of the categories.