Overall-survival analysis of a TCGA cohort — tcga

Downloads (or loads) a TCGA dataset, normalises it, stratifies patients into high and low expressers of a gene or signature (upper vs lower quartile), and runs a Kaplan-Meier overall-survival analysis.

Usage

tcga_survival(
  TCGA.dataset,
  gene.signature,
  gene.name = NULL,
  rda.file.path = NULL,
  plot.dir = "figures/",
  data.dir = "data/"
)

Arguments

TCGA.dataset: TCGA project id, e.g. "TCGA-LAML".
gene.signature: Gene, or vector of genes, defining the signature. With several genes the ranking score is the mean z-score (see stratify_by_expression()).
gene.name: Optional label (defaults to gene.signature).
rda.file.path: Optional path to a prepared .rda from download_tcga_rnaseq(); if NULL, the data are downloaded.
plot.dir: Directory to save the survival plot into.
data.dir: Directory for downloaded and normalised data.

Value

Invisibly, the clinical table with the Signature (High / Low) assignment. The survival plot is written to plot.dir.

Examples

if (FALSE) { # \dontrun{
tcga_survival("TCGA-LAML", gene.signature = "TLR2")
} # }