Question: survival analysis of tcga clinical data
0
gravatar for akutasame
5 days ago by
akutasame20
United Kingdom
akutasame20 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 • 93 views
ADD COMMENTlink modified 3 days ago • written 5 days ago by akutasame20

That was helpful, Thank you

ADD REPLYlink written 3 days ago by akutasame20
1
gravatar for MatthewP
5 days ago by
MatthewP320
China
MatthewP320 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 5 days ago by MatthewP320
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