TCGA2STAT (version 1.0)

TumorNormalMatch: Get Matched Tumor and Normal Samples.

Description

Get data matrix of molecular profiles for matching tumor and normal samples.

Usage

TumorNormalMatch(tcgad)

Arguments

tcgad

data object returned by getTCGA function.

Value

• A list of two elements:
• primary.tumor
  a matrix containing tumor samples; of dimension of gene x tumor samples.
• normal
  a matrix of normal samples; of dimension gene x normal samples.
• Note: For methylation data, each row is a probe for CpG island, and the first three columns are the gene symbol, chromosome, and genome coordinate.

Details

This function returns a list of two gene-by-sample matrices. The samples in both matrices are of matching patients and are sorted at the same order.

Examples

library(TCGA2STAT)

lusc.rnaseq2 <- getTCGA(disease="LUSC", data.type="RNASeq2")
lusc.rnaseq2.tum.norm <- TumorNormalMatch(lusc.rnaseq2)