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Bioinformatics with R Cookbook by Paurush Praveen Sinha

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Running association scans for SNPs

The previous recipe presented the approach to discover the dependence of a phenotype on a single SNP. However, in the case of phenotypes such as complex diseases, one has to keep an eye on all of the SNPs and scan the entire set. This recipe will discuss computing the significance of the dependence of phenotypes on all SNPs available in the data.

Getting ready

In this recipe, we will continue working on the same dataset of SNPs and the same SNPassoc library as the previous recipe. We will directly use the SNP object, mySNP, created previously.

How to do it…

We start our recipe step from the point where we created the SNP object named mySNP. This time, we try to understand another phenotype, say, the protein level. ...

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