5  Further resources

Here I list some resources you can check to perform your analysis.

5.1 PCA

To do PCA on R I highly recommend to use the package PCAtools from Kevin Blighe:

https://bioconductor.org/packages/release/bioc/html/PCAtools.html

With this package one can use metadata to customize the PCA biplots.

To do a pairs plot you can either use the function pairsplot from the package PCAtoolsor the function ggpairs from the package GGally.

5.2 Survival analysis

A very good starter to survival analysis can be found in this page:

http://www.sthda.com/english/wiki/survival-analysis-basics

They describe the basics of survival analysis and how to use the packages survival and survminer.

And in the next post, they explain the cox proportional hazards model.

http://www.sthda.com/english/wiki/cox-proportional-hazards-model

Highly recommend to use this when doing survival analysis, as you get estimates for your comparisons and confidence intervals.