View source: R/load.cancer.datasets.R
load.cancer.datasets | R Documentation |
Returns a list of lists containing all cancer meta-analysis datasets
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 )
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 |
Returns a meta-analysis list of lists
Syed Haider & Paul C. Boutros
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 );
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