TCGA_Preprocess_DNAmethylation: The TCGA_Preprocess_DNAmethylation function

In gevaertlab/EpiMix: EpiMix: an integrative tool for the population-level analysis of DNA methylation

The TCGA_Preprocess_DNAmethylation function

Description

Pre-processes DNA methylation data from TCGA.

Usage

TCGA_Preprocess_DNAmethylation(
  CancerSite,
  METdirectories,
  doBatchCorrection = FALSE,
  batch.correction.method = "Seurat",
  MissingValueThreshold = 0.2,
  cores = 1,
  use450K = FALSE
)

Arguments

CancerSite	character string indicating the TCGA cancer code.
METdirectories	character vector with directories with the downloaded data. It can be the object returned by the TCGA_Download_DNAmethylation function.
doBatchCorrection	logical indicating whether to perform batch correction. Default: False.
batch.correction.method	character string indicating the method to perform batch correction. The value should be either 'Seurat' or 'Combat'. Default: 'Seurat'. Note: Seurat is much faster than the Combat.
MissingValueThreshold	numeric values indicating the threshold for removing samples or genes with missing values.Default: 0.2.
cores	integer indicating the number of cores to be used for performing batch correction with Combat.
use450K	logic indicating whether to force use 450K, instead of 27K data.

Details

Pre-process includes eliminating samples and genes with too many NAs, imputing NAs, and doing Batch correction. If there are samples with both 27k and 450k data, the 27k data will be used only if the sample number in the 27k data is greater than the 450k data and there is more than 50 samples in the 27k data. Otherwise, the 450k data is used and the 27k data is discarded.

Value

pre-processed methylation data matrix with CpG probe in rows and samples in columns.

Pre-processed methylation data matrix with CpG probe in rows and samples in columns.

Examples

METdirectories <- TCGA_Download_DNAmethylation(CancerSite = 'OV', TargetDirectory = tempdir())
METProcessedData <- TCGA_Preprocess_DNAmethylation(CancerSite = 'OV',
                                                   METdirectories = METdirectories)

gevaertlab/EpiMix documentation built on July 20, 2023, 9:28 a.m.