two-sample survival comparison dependent on mutation present in gene

two-sample survival comparison dependent on mutation present in gene

two_sample_surv_setup(sym, se, timevar = "OS.Time", eventvar = "OS.event")

Arguments

sym

character(1) HUGO symbol

se

a SummarizedExperiment instance with ragged mutation matrix as assay

timevar

character(1) variable found in colData(se) recording time to event

eventvar

character(1) variable found in colData(se) recording death or censoring

Examples

data(brcamutSE)
ss = two_sample_surv_setup("TTN", brcamutSE)
summary(ss)
#> Call:
#> survival::survdiff(formula = f)
#> 
#> n=793, 184 observations deleted due to missingness.
#> 
#>             N Observed Expected (O-E)^2/E (O-E)^2/V
#> grp=FALSE 637       64     71.2     0.738       3.9
#> grp=TRUE  156       24     16.8     3.138       3.9
#> 
#>  Chisq= 3.9  on 1 degrees of freedom, p= 0.05 
plot(ss, lty=1:2, lwd=2)
legend(500,.4,  lty=1:2, lwd=2, legend=c("TTN WT", "TTN Mut"))