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Bioinformatics with R Cookbook by Paurush Praveen Sinha

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Data handling with the GWASTools package

We have dealt with two different data formats. In this recipe, we will introduce an R package that not only enables us to work with raw data but also helps in quality checks and many analytical steps. In this recipe, we will mainly talk about handling raw data and quality checks with GWASTools.

Getting ready

For this recipe, we will use the GWASTools package and the included data sets for demonstration purposes. Besides this, we will also use the data package named GWASdata.

How to do it...

Perform the following steps to walk through the use of the GWASTools package to work with GWAS data:

  1. Start with installing the package from the Bioconductor repository by typing the following commands:
    > source("http://bioconductor.org/biocLite.R") ...

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