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Bioinformatics with R Cookbook by Paurush Praveen Sinha

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Useful visualizations for MS data analysis

In this recipe, we will try out some interesting visualizations for MS data. The visualizations we will look at include peak labeling visualization, multiple spectra plotting, and fragment ion visualization.

Getting ready

We will use the same data and libraries that we have already used in our previous recipes.

How to do it…

To create some useful visualizations for MS or proteomic data analysis, perform the following steps:

  1. First, start by labeling the peaks in your MS datasets. Here, you will label the top 10 spectra in your plot with their masses.
  2. Load the MALDIquant library and the fiedler2009subset data as follows:
    > library("MALDIquant")
    > data("fiedler2009subset", package = "MALDIquant")
    
  3. Use only the ...

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