Fit Kaplan-Meier survival model stratifying patients based on INCOMMON classes, for a single gene and tumour type.

Usage

kaplan_meier_fit(x, tumor_type, gene, survival_time, survival_status)

Arguments

x: An object of class 'INCOMMON' containing the classification results as produced by function classify.
tumor_type: The tumor type of patients to stratify.
gene: The gene on which patient's stratification is based.
survival_time: The variable in clincal_data to be used as survival time.
survival_status: The variable in clincal_data to be used as survival status.

Value

An object of class 'INCOMMON' containing an additional object survival.

Examples

# First load example classified data
data(MSK_classified)
# Perform survival analysis based on the classification of KRAS mutant samples of pancreatic adenocarcinoma
MSK_classified = kaplan_meier_fit(x = MSK_classified, tumor_type = 'PAAD', gene = 'KRAS', survival_time = 'OS_MONTHS', survival_status = 'OS_STATUS')
#> ℹ There are 20289 different genotypes
#> ℹ The most abundant genotypes are:
#> • Mutant TP53 with LOH (562 Samples, Frequency 0.02)
#> • Mutant KRAS without AMP (199 Samples, Frequency 0.01)
#> • Mutant KRAS without AMP,Mutant TP53 with LOH (149 Samples, Frequency 0.01)
#> Call: survfit(formula = "survival::Surv(OS_MONTHS, OS_STATUS) ~ group", 
#>     data = data)
#> 
#>    6 observations deleted due to missingness 
#>                           n events median 0.95LCL 0.95UCL
#> KRAS WT                 109     63   21.5   18.86    30.8
#> Mutant KRAS without AMP 940    565   17.2   15.74    19.4
#> Mutant KRAS with AMP    667    457   11.2    9.69    12.5