loadBreastDatasets: Function to load breast cancer SummarizedExperiment objects...
In bhklab/MetaGxBreast: Transcriptomic Breast Cancer Datasets

This function returns breast cancer datasets from the hub and a vector of patients from the datasets that are duplicates based on a spearman correlation > 0.98

loadBreastDatasets(
  rescale = FALSE,
  minNumberGenes = 0,
  minNumberEvents = 0,
  minSampleSize = 0,
  keepCommonOnly = FALSE,
  imputeMissing = FALSE,
  removeDuplicates = FALSE
)

`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 a summarizedExperiment (default 0)
`keepCommonOnly`	remove entrezIDs not common to all datasets (default FALSE)
`imputeMissing`	remove patients from datasets with missing expression values
`removeDuplicates`	remove patients with a Spearman correlation greater than or equal to 0.98 with other patient expression profiles (default TRUE)

A 'list' with 2 elements. The First element named 'SummarizedExperiment's 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).

bhklab/MetaGxBreast documentation built on April 29, 2021, 5:20 p.m.