plot_km: Basic survival analysis plot

In pmartR/pmartRqc: Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data

Basic survival analysis plot

Description

Implements overall survival analysis or progression-free survival analysis, depending upon the datatypes supplied to surv_designation, and plot the resulting Kaplan-Meier curve.

Usage

plot_km(omicsData)

Arguments

omicsData

A pmartR data object of any class, which has a 'group_df' attribute that is usually created by the 'group_designation()' function

Value

a Kaplan-Meier curve

Examples

## Not run: 
library(MSomicsSTAT)
library(OvarianPepdataBP)
attr(tcga_ovarian_pepdata_bp, "survDF") <- list(t_death = "survival_time",
                                                ind_death = "vital_status")
plot_km(omicsData = tcga_ovarian_pepdata_bp)

# Add covariates to "survDF" attribute
attr(tcga_ovarian_pepdata_bp, "survDF") <- list(
  t_death = "survival_time",
  ind_death = "vital_status",
  covariates = "age_at_initial_pathologic_diagnosis"
)
plot_km(omicsData = tcga_ovarian_pepdata_bp)

## End(Not run)

pmartR/pmartRqc documentation built on March 4, 2024, 3:46 p.m.