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PoisonAlien / maftools

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
http://bioconductor.org/packages/release/bioc/html/maftools.html
MIT License
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Error when using mafSurvival with TCGA samples #1073

Closed Mars-fi closed 4 days ago

Mars-fi commented 4 days ago

There is an error when using mafSurvival in TCGA-PAAD cohort, the K-M plot didn't exist.

Command mafSurvival(maf=maf, genes=c("KRAS"), time="days_to_last_follow_up", Status="days_to_death", isTCGA=TRUE)

Session info Looking for clinical data in annoatation slot of MAF.. Number of mutated samples for given genes: KRAS 106 Removed 142 samples with NA's Median survival.. Group medianTime N

1: Mutant 131.5 16 2: WT 141.0 14 Error: survfit.formula(formula = survival::Surv(time = Time, event = Status) ~ : data set has no non-missing observations Warning: In survival::Surv(time = Time, event = Status) : Invalid status value, converted to NA Thank you!
PoisonAlien commented 4 days ago

Hi,

How did you generate the maf? Is it via tcgaLoad() function?

Mars-fi commented 4 days ago

no, I just use read.maf()

Besides, I have already solved this problem by replacing the vital_status with Dead=1, Alive=0.

Thank you very much!