simpleSurvival: Simple Survival

In weshorton/wrh.rUtils: Miscellaneous R Utility Functions

Simple Survival

Description

Calculate Kaplan Meier survival estimate and plot. Split groups based on expression.

Usage

simpleSurvival(
  data_dt,
  exprCol_v,
  timeCol_v = "OS.time",
  deathCol_v = "OS",
  method_v = "quartile",
  outputFile_v = NULL,
  name_v = NULL
)

Arguments

data_dt	data.table with combined clinical and expression data
exprCol_v	column that contains expression information to use as a group divider.
timeCol_v	column that indicates survival time. Originally was days_to_death, may now be OS.time or DSS.time
deathCol_v	column that indicates death (vital) status. "DECEASED" == 1; "LIVING" == 0
method_v	which method to use to divide expression groups. quartile (default) will take the upper and lower quartiles. Median will split in half on the median.
outputFile_v	optional path to an output location if saving file is desired
name_v	optional name to add to the title. Usually the title of the dataset used as input.

Details

This function is specifically made for data that has been downloaded from the TCGA hub by the UCSCXenaTools package. [here](https://xenabrowser.net/datapages/?dataset=survival dataset that is accessed by this tool. There are multiple survival classifications in these datasets: 1. OS: overall survival 2. DSS: disease-specific survival 3. DFI: disease-free interval 4. PFI: progression-free interval

Value

plot

weshorton/wrh.rUtils documentation built on Feb. 6, 2025, 5:30 a.m.