Question: survival analysis of tcga clinical data
2
gravatar for akutasame
9 months ago by
akutasame40
United Kingdom
akutasame40 wrote:

Hi all,

I want to do survival analysis of clinical data but I am not sure about censoring TCGA clinical data? I have ''daysto_lastfollowup", "daysto_death", "vital status" and "overall_survival_months". What I did is

Method 1:

daysToEvent <- rep(NA, nrow(tcgaClinical))
daysToEvent[vitalStatus == "Alive"] <- daysToLastFollowup[vitalStatus == "Alive"]
daysToEvent[vitalStatus == "Dead"] <- daysToDeath[vitalStatus == "Dead"]
eventStatus <- rep(NA, nrow(tcgaClinical))
eventStatus[vitalStatus == "Alive"] <- 1
eventStatus[vitalStatus == "Dead"] <- 0

tcgaOS <- Surv(daysToEvent/30, eventStatus == 0)
rownames(tcgaOS) <- rownames(tcgaClinical)

Or

Method 2:

eventStatus <- rep(NA, nrow(tcgaClinical))
eventStatus[vitalStatus == "Alive"] <- 1
eventStatus[vitalStatus == "Dead"] <- 0

tcgaOSM <- Surv(tcgaClinical$OS_MONTHS, eventStatus == 0)
rownames(tcgaOSM) <- rownames(tcgaClinical)

Which method makes more sense ? Thank you

clinical survival tcga • 1.1k views
ADD COMMENTlink modified 9 months ago • written 9 months ago by akutasame40

That was helpful, Thank you

ADD REPLYlink written 9 months ago by akutasame40
3
gravatar for MatthewP
9 months ago by
MatthewP710
China
MatthewP710 wrote:

Hello, I recommend you download clinical data from cBioPortal instead of TCGA/GDC. If you download clinical data from cBioPortal you will see fields Overall Survival (Months) and Overall Survival Status thats what you need for OS(Overall survival) analysis.

As OS the event is dead, so alive is censored data, you should give value 1 to dead and 0 to alive. However I recommend use 1 and 2, give value 2 to dead and 1 to alive.

Here, some tutorial may be useful for you:
https://www.emilyzabor.com/tutorials/survival_analysis_in_r_tutorial.html#introduction
https://www.datacamp.com/community/tutorials/survival-analysis-R
http://www.sthda.com/english/wiki/survival-analysis-basics

ADD COMMENTlink written 9 months ago by MatthewP710
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