How can I use R to do many genes survival analysis at the same time?

Question

[137737756]

I plan to use the DESeq2::rlog transformed TCGA HTseq_counts data and the TCGA clinical data to do survival analysis. But I am confused how to do many genes(>10000) survival analysis at the same time.

I would be grateful if you could give insights.

Thank you!!

[zx8754]

Try to do it for one gene, then wrap it in a loop?

[Kevin Blighe]

To follow on from that, you may consider just looping over the formula for Cox proportional hazards to see which genes are statistically significant from that (and then plotting the curves for those). the Cox proportional hazards model is implemented via coxph in R: A: cox proportional hazard model

Answer 1

[huynguyen96.dnu]

Hi! now you can do this task very easily with my recently developed tool named 'geneSA' (https://github.com/huynguyen250896/geneSA). Give it a try ;)

[Shernan]

Thanks so much for posting this tool! I was able to get it to run on my dataset, but the output table has no results. Have you ever encountered that problem? Thanks in advance!