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_PAAD_output)
# Perform survival analysis based on the classification of KRAS mutant samples of pancreatic adenocarcinoma
MSK_PAAD_output = kaplan_meier_fit(x = MSK_PAAD_output, tumor_type = 'PAAD', gene = 'KRAS', survival_time = 'OS_MONTHS', survival_status = 'OS_STATUS')
#> Joining with `by = join_by(id)`
#> Call: survfit(formula = "survival::Surv(OS_MONTHS, OS_STATUS) ~ group", 
#>     data = data)
#> 
#>    7 observations deleted due to missingness 
#>                   n events median 0.95LCL 0.95UCL
#> WT              214     92   38.3   28.98    51.1
#> Low Dosage      541    344   17.4   15.34    19.8
#> Balanced Dosage 670    417   14.6   13.34    15.8
#> High Dosage     347    237   10.7    9.36    12.5