load.datasets {iDOS}

load.datasets

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")
  );