TCGA2STAT (version 1.0)

SampleSplit: Split the Data by Sample Types.

Description

Split the TCGA data into data matrices of different sample types (normal, tumor, or recurrent tumor).

Usage

SampleSplit(dat)

Arguments

dat

data matrix in gene x sample format.

Value

• A list of three elements:
• primary.tumor
  a matrix of tumor samples of dimension gene x sample.
• recurrent.tumor
  a matrix of recurrent tumor samples of dimension gene x sample.
• normal
  a matrix from normal samples of dimension gene x sample.
• 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.

Examples

library(TCGA2STAT)
lusc.rnaseq2 <- getTCGA(disease="LUSC", data.type="RNASeq2")
lusc.rnaseq2.bytype <- SampleSplit(lusc.rnaseq2)