load.datasets: load.datasets

In iDOS: Integrated Discovery of Oncogenic Signatures

Description

Function to load and systemise molecular datasets

Usage

load.datasets(
  data.dir = "./", 
  metadata = NULL, 
  data.types = c("mRNA.T", "ann")
  )

Arguments

data.dir	Path to base data directory or directory containing molecular profiles
metadata	Dataset by profile metadata matrix containing file names of the molecular profiles for different datasets
data.types	Datatypes to be read Valid datatypes are: mRNA.T, mRNA.N, CNA (includes: log2, calls and fractions), annotations

Value

List of lists containing datasets and respective molecular profiles as matrices

Author(s)

Syed Haider

Examples

# locate test data directory which comes with the package
data.dir <- paste(system.file("programdata/testdata/", package = "iDOS"), "/", sep = "");

# read meta data file
metadata <- read.table(
  file = paste(data.dir, "metadata.txt", sep = ""), 
  row.names = 1, 
  header = TRUE, 
  sep = "\t",
  stringsAsFactors = FALSE
  );

x <- load.datasets(
  data.dir = data.dir,
  metadata = metadata,
  data.types = c("mRNA.T", "mRNA.N", "ann")
  );

iDOS documentation built on May 2, 2019, 2:28 p.m.