loadOvarianEsets: Function to load ovarian cancer expression sets from the...

In bhklab/MetaGxOvarian: Transcriptomic Ovarian Cancer Datasets

Description

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

Usage

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

Arguments

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

Value

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).

Examples

esetsAndDups = loadOvarianEsets()

bhklab/MetaGxOvarian documentation built on Aug. 14, 2021, 1:59 p.m.