load.cancer.datasets {SIMMS}

Load all cancer meta-analysis datasets

Description

Returns a list of lists containing all cancer meta-analysis datasets

Usage

load.cancer.datasets(
  tumour.only = TRUE,
  with.survival.only = TRUE,
  truncate.survival = 100,
  datasets.to.load = "all",
  data.types = c("mRNA"),
  datasets.file = "datasets.txt",
  data.directory = ".",
  verbose = FALSE,
  subset = NULL
)

Arguments

tumour.only

Logical indicating if we should only load tumour samples (TRUE, the default)

with.survival.only

Logical indicating if we should only load samples with survival data (TRUE, the default)

truncate.survival

A numeric value specifying survival truncation in years. Defaults to 100 years which effectively means no truncation

datasets.to.load

A vector of datasets to be loaded. If 'all', then all available datasets are loaded

data.types

A vector of molecular datatypes to load. Defaults to c('mRNA')

datasets.file

A file in data.directory containing a listing of all usable datasets

data.directory

A directory containing all data-files to be loaded

verbose

Logical indicating whether or not status messages should be given

subset

A list with a Field and Entry component specifying a subset of patients to be selected whose annotation Field matches Entry

Value

Returns a meta-analysis list of lists

Author(s)

Syed Haider & Paul C. Boutros

Examples

data.dir <- get.program.defaults()[["test.data.dir"]];
x1 <- load.cancer.datasets(
  datasets.to.load = c('Breastdata1'),
  data.types = c("mRNA"),
  data.directory = data.dir
  );