How can I use R to do many genes survival analysis at the same time?
1
1
Entering edit mode
3.9 years ago
137737756 ▴ 10

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!!

survival data

RNA_seq data

R TCGA survival RNA-Seq • 3.1k views
ADD COMMENT
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
9 months ago

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 ;)

ADD COMMENT
0
Entering edit mode

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!

ADD REPLY

Login before adding your answer.

Traffic: 1269 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6