Question: Integrating methylation in survival analysis
gravatar for Pin.Bioinf
11 months ago by
Pin.Bioinf250 wrote:

Hello, I am trying to do a survival analysis with TCGA data following this tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data , but I want to integrate methylation data instead of rnaseq data. What I am doing is selecting the gene of interest and averaging its CpG beta values per column: then, I create a vector for that gene where, for samples where avg beta values are >0.3 , the value is a 1, and a 0 if its <0.3. Then, my survival function is as follows:

s <- survfit(Surv(as.numeric(as.character(all_clin$new_death))[ind_clin],all_clin$death_event[ind_clin])~event_r[ind_clin])
s1 <- tryCatch(survdiff(Surv(as.numeric(as.character(all_clin$new_death))[ind_clin],all_clin$death_event[ind_clin])~event_r[ind_clin]), error = function(e) return(NA))

where event_r is a vector of 1s and 0s for the corresponding clinical samples in that gene of interest.

Do you think averaging the beta-values for the whole gene is a good approach to integrate methylation with survival? Any other suggestions? Thank you

rna-seq survival methylation R • 419 views
ADD COMMENTlink written 11 months ago by Pin.Bioinf250

I agree with @Kevin you should perform cox for each and every probe separately. This will lead you to identify probable prognostic CpG sites.

ADD REPLYlink written 5 months ago by Researcher40
gravatar for Kevin Blighe
11 months ago by
Kevin Blighe47k
Kevin Blighe47k wrote:

I think that you should treat the methylation probes as separate entities.

ADD COMMENTlink written 11 months ago by Kevin Blighe47k

Okay, I will try that approach. Thank you!

ADD REPLYlink written 11 months ago by Pin.Bioinf250

But would averaging the beta values be recommended, can't we consider the continuous values for each probe?

ADD REPLYlink written 6 months ago by Researcher40

I replied to you in the other thread: A: Survival analysis with gene expression

ADD REPLYlink written 6 months ago by Kevin Blighe47k
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