create.survobj: Utility function for loading meta-analysis lists

In SIMMS: Subnetwork Integration for Multi-Modal Signatures

Utility function for loading meta-analysis lists

Description

Create Surv objects from an annotation-matrix with handling for different time units.

Usage

create.survobj(annotation = NULL, truncate.survival = 100)

Arguments

annotation	A patient annotation matrix (patients = rows) with (at least) columns for survtime, survstat, and survtime.unit
truncate.survival	A numeric value specifying survival truncation in years. Defaults to 100 years which effectively means no truncation

Value

Returns an object of class Surv

Author(s)

Paul C. Boutros

Examples

annotation.file <- paste(
  get.program.defaults()[["test.data.dir"]],
  "/Breastdata2/patient_annotation.txt", sep = ""
  );
annotation <- read.table(
  annotation.file,
  header = TRUE,
  row.names = 1,
  sep = "\t"
  );

# select the appropriate survtime and survstat variable for this dataset
annotation$survstat      <- annotation[,'e.dfs'];
annotation$survtime      <- annotation[,'t.dfs'];
annotation$survtime.unit <- annotation[,'t.dfs.unit'];

# only keep samples with survival data
annotation <- annotation[!is.na(annotation$survstat) & !is.na(annotation$survstat),];

surv.obj <- create.survobj(annotation = annotation);

SIMMS documentation built on April 24, 2022, 5:06 p.m.