Question: How can I use R to do many genes survival analysis at the same time?
1
gravatar for 137737756
2.1 years ago by
13773775610
13773775610 wrote:

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

rna-seq survival tcga R • 1.4k views
ADD COMMENTlink modified 2.1 years ago by zx87549.4k • written 2.1 years ago by 13773775610
1

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

ADD REPLYlink written 2.1 years ago by zx87549.4k

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 REPLYlink written 2.1 years ago by Kevin Blighe63k
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