problem for gene survival analysis through “Survival” package in R

problem for gene survival analysis through “Survival” package in R



My data belong to subtype of TCGA breast cancer. I have to do survival analysis for this data set. I know “survival” package but I don’t know how can I involve genes profiles to survival analysis. Surly, for OS analysis, I can use “survfit” as a function for survival analysis and by “Time” and “OS status” I can get my target. but really, I don’t know how to input my transcriptom profile as input in my survival analysis. In other words, I want to know how can I gene survival analysis through “survival” package or another nice package. due to this research, I found “RTCGA” as a bioconductor package but it’s not possible to customize arguments of “survivalTCGA” for for survival analysis about subtype of breasat cancer.
I deeply appreciate if you share your comment with me.

Best Regards,

Mohammad Darzi


Survival Analysis

Gene Survival Analysis



I do survival analysis with (patient) consensus cluster as a independent variable explaining survival time. This is an example.

coxph(Surv(time = Time, event = Death) ~ as.factor(myresults$consensuscluster), data = myresults, ties = "exact")

Perhaps this helps. I’d cluster your data first which assigns clusters to every patient, then go from there. Then the genes associating with a cluster can be analysed separately. Good class discovery/ clustering packages in my experiments on a single platform have been CLEST and M3C.

updated 2.7 years ago by


written 2.7 years ago by



The main strategy here is to first use the information of the gene to stratify the patients into different groups (for example: High gene expression group vs. Low gene expression group, or Mutated gene group vs. Non-mutated gene group, etc)and only then perform the survival analysis. Then call the following survfit() function

survfit(Surv(OS_time, VitalStatus == 1) ~ Patient_group, data=df)

OS_time: overall survival time;
Vital Status (Dead=1, Alive=0),
Patient_group: Grouping of patient using information of the gene of interest.
df=your data frame containing the data.

Hi! now you can do this task very easily with my recently developed tool named ‘geneSA’ ( Its output will automatically report genes statistically significant with survival outcome. Give it a try 😉

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