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Bioinformatics with R Cookbook by Paurush Praveen Sinha

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The whole genome SNP association analysis

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.

Getting ready

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.

How to do it…

Follow the ensuing steps to perform a whole genome association analysis for SNPs:

  1. Start with loading the HapMap data as follows:

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