loadOvarianEsets: Function to load ovarian cancer expression sets from the...
In mzon7/MetaGxOvarian: Transcriptomic Ovarian Cancer Datasets

Description Usage Arguments Value Examples

This function returns ovarian cancer datasets from the hub and a vector of patients from the datasets that are most likely duplicates

loadOvarianEsets(removeDuplicates = TRUE, quantileCutoff = 0,
  rescale = FALSE, minNumberGenes = 0, minNumberEvents = 0,
  minSampleSize = 0, removeRetracted = TRUE, removeSubsets = TRUE,
  keepCommonOnly = FALSE, imputeMissing = FALSE)

`removeDuplicates`	remove patients with a Spearman correlation greater than or equal to 0.98 with other patient expression profiles (default TRUE)
`quantileCutoff`	A nueric between 0 and 1 specifying to remove genes with standard deviation below the required quantile (default 0)
`rescale`	apply centering and scaling to the expression sets (default FALSE)
`minNumberGenes`	an integer specifying to remove expression sets with less genes than this number (default 0)
`minNumberEvents`	an integer specifying how man survival events must be in the dataset to keep the dataset (default 0)
`minSampleSize`	an integer specifying the minimum number of patients required in an eset (default 0)
`removeRetracted`	remove datasets from retracted papers (default TRUE, currently just PMID17290060 dataset)
`removeSubsets`	remove datasets that are a subset of other datasets (defeault TRUE, currently just PMID19318476)
`keepCommonOnly`	remove probes not common to all datasets (default FALSE)
`imputeMissing`	remove patients from datasets with missing expression values

a list with 2 elements. The First element named esets contains the datasets. The second element named duplicates contains a vector with patient IDs for the duplicate patients (those with Spearman correlation greater than or equal to 0.98 with other patient expression profiles).