Search code examples
rcluster-analysisk-meanssurvival-analysis

k-means clustering with survival Data

just a basic question concerning k-means clustering analysis on survival data, like this one:

enter image description here

I am doing k-means clustering to identify clusters which Gene influences the survival most... However do I include the survival time into my k-means function or should I leave it out? So should I put it into the kmeans() function e.g. in R?

Kind regards,

Hashriama

Solution

  • I think that your approach is not the best one. Your goal is to select genes associated with censored/uncensored survival. The use of supervised methods seems the most suitable. Using a k-means will only cluster genes by similarities without regard to survival, and even if you wanted to add survival in your modeling it would not make sense because you are omitting censoring.

    There are Cox regressions to which an L1 penalty is added, allowing variable selection without omitting censoring. This kind of approach seems more appropriate to accomplish your goal and fits better in your context. To learn more, here is an article from Jiang Gui & Hongzhe Li that uses penalized Cox regression (look at the R package biospear too if needed): https://academic.oup.com/bioinformatics/article/21/13/3001/196819