fit_surv: Basic survival analysis function

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

Basic survival analysis function

Description

Implements overall survival analysis or progression-free survival analysis, depending upon the datatypes supplied to surv_designation, and return the "survfit" object

Usage

fit_surv(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

if fitted survival analysis object is returned

Examples

## Not run: 
library(MSomicsSTAT)
library(OvarianPepdataBP)

# Basic analysis without covariates
attr(tcga_ovarian_pepdata_bp, "survDF") <- list(t_death = "survival_time",
                                                ind_death = "vital_status")
sfit <- fit_surv(tcga_ovarian_pepdata_bp)
plot(sfit)

# Add some covariate information
attr(tcga_ovarian_pepdata_bp, "survDF") <- list(
  t_death = "survival_time",
  ind_death = "vital_status",
  covariates = "g__initial_pathologic_diagnosis_method_g1"
)
sfit <- fit_surv(tcga_ovarian_pepdata_bp)
plot(sfit, col = c(1, 2))

## End(Not run)

pmartR/pmartRqc documentation built on April 25, 2024, 6:18 a.m.