It's an unavoidable fact of bioinformatics life that we spend a lot of time converting between file formats. In this brief recipe, we'll look at some convenient methods in R, that allows us to convert between MS data formats.
Converting MS formats to move data between tools
Getting ready
For this recipe, we require the mzR package and the threonine_i2_e35_pH_tree.mzXML file from the datasets/ch6 folder of this book's repository. Some of the dependencies rely on encapsulated Java code, so you'll need to install a Java Runtime Environment (JRE) for your system; refer to https://docs.oracle.com/goldengate/1212/gg-winux/GDRAD/java.htm for instructions. Install the JRE before the R packages.
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