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Bioinformatics with R Cookbook by Paurush Praveen Sinha

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The SNP association analysis

GWAS has gained popularity as an approach to identify genetic variants associated with a disease phenotype. This is accomplished through statistical analysis of the GWAS data. These methods of statistical analyses attempt to establish the association between each individual SNP and the observed phenotype. In this recipe, we will perform such an association analysis.

Getting ready

To prepare for a GWAS analysis, we need data that contains all the information explained earlier. In this recipe, we will use the data available in packages. While going through the recipe, we will introduce the corresponding packages.

How to do it…

Perform the following steps to explain the SNP association analysis with diseases or other phenotypes: ...

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