COMPLETE SURVIVAL ANALYSIS tutorial in R: Kaplan-Meier, Cox regression, Forest Plots...

In this tutorial, I will explain how to perform survival analysis in R, including log rank test, Cox regression, Kaplan-Meier curves, and more! We will use the R packages ggsurvplot, survminer and survival. You will learn how to:
- plot a Kaplan Meier curve
- test for differences between groups using the log rank test
- build a survival model with Cox regression
- and visualise your results with a forest plot.
And as always, you can find the code I am using in this tutorial at biostatsquid.com, where you can also find a step by step explanation of the code. For this tutorial you will need R, or Rstudio, and you will need to install the package listed above.
Hope you like it!
biostatsquid.c...
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Other interesting resources for survival analysis:
Easy R tutorial: www.sthda.com/e...
More on survival curves: www.ibm.com/do...

[@biostatsquid]

Find all the code used in this tutorial here: biostatsquid.com/easy-survival-analysis-r-tutorial/

[@ZaguY06]

Thank you so much for this video! I have a question regarding the forest plot of the cox regression, can we add the global p-value (summary) to the forest plot? is there any way? I would appreciate your help with this!

[@biostatsquid]

Hey! Thanks for your comment, I'm glad it was useful:) The global p-value should be already there, in the bottom of the plot. If you'd like it somewhere else, you can easily extract it from the object as a variable (assign it to gloabl_p_val or similar), and then use annotate() as you would to annotate a ggplot object! Hope this helps:)

[@hamzavanderross1235]

Thanks! This is really helpful!

[@ArezouRahimi]

Hi I have this error Error in `GetAssayData()`: ! GetAssayData doesn't work for multiple layers in v5 assay. Backtrace: 1. Seurat::IntegrateData(...) 2. Seurat:::PairwiseIntegrateReference(...) 5. SeuratObject:::GetAssayData.Seurat(object = object.1, slot = "data") 7. SeuratObject:::GetAssayData.StdAssay(object = object[[assay]], layer = layer) with this code combined_seurat

[@biostatsquid]

Hi - that's probably because you are using Seurat v5, instead of v4 (which is the one I use). You can either use v4, or use LayerData() function if you would like to stick with v5 - check this: github.com/satijalab/seurat/issues/8304

[@evissima107]

This squid's videos help me a LOT during my PhD. It saves me so much time. Thank you so much for uploading this content!! Keep it up!! I'm another biostatsquid fan :)

[@ThomasMcDonnell-x3f]

This is fantastic! You're a great teacher. Please could you do logistic regression and ROC analysis next?

[@reregad590]

This was very helpful, your way of teach just keep me engaged and understanding, thanks ❤

[@alex146]

Actually a really good video and the channel!

[@biostatsquid]

Thank you!

[@sanjaisrao484]

Thank you very much, You are amazing

[@biostatsquid]

Thank you! Glad it was useful:)

[@ipgrulles]

thank you