So far, we have worked with SNP data where we had a few SNPs and made attempts to understand the phenotype dependence on these SNPs. However, we are yet to cover the most interesting part of association analysis, which is the whole genome analysis. Here, we attempt to study the association analysis of a trait across the whole genome. This recipe is an attempt at doing such an analysis.
Until now, we have been using a small data set. Now, we switch to a much larger one called the
HapMap data set. The data is available within the
SNPassoc package of R.
Follow the ensuing steps to perform a whole genome association analysis for SNPs:
HapMapdata as follows: