I'm looking for some assistance in statistical analysis with R, but also some general stats advice.
I am analysing cardiac phenotype data by comparing 2 groups. The 2 groups are unmatched individuals, but within each group, they are clustered in family subgroups (of between 1 and ~6).
I want to report the difference in prevalence of a specific ECG appearance (binary - i.e. either present or absent in each individual) between the 2 groups.
For example:
Group 1 consists of 157 individuals comprised of 41 family clusters
Group 2 consists of 463 individuals comprised of 163 family clusters
Prevalence of x in Group 1 = 22.9%
Prevalence of x in Group 2 = 24.6%
Group 1 are cases and Group 2 controls (i.e. not randomized)
What test is most appropriate in this circumstance, and which package in R provides the easiest way to account for the clustering of relatives within families?
Having looked around, I have found:
  • Ratio estimate chi-square test
  • Generalized estimating equation

But I have no experience of either of these techniques, and can't find any examples of their use in R.
Can anyone help?
(PS: This is not homework)