I'm not an expert but Rafael Irizarry's book titled "Introduction to data science" is definitely a great source to start with. Here is the book: https://leanpub.com/datasciencebook The man himself illustrates it in these videos: https://www.edx.org/professional-certificate/harvardx-data-science
Once you've built a background, contact me and I may help with more advanced resources.
The beauty with R is its flexibility as applied to any project. CRAN (https://cran.r-project.org) have list of interesting materials as regards the use and application of the various packages and integrations. Since you are looking at machine learning i have personally used this book and it proved to be a good resource.
https://www.packtpub.com/product/practical-machine-learning-with-r/9781838550134