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

Description Usage Arguments Value Examples

View source: R/loadOvarianEsets.R

Description

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

Usage

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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

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esetsAndDups = loadOvarianEsets()

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