Preprocess_MAdata_Cancer: The Preprocess_MAdata_Cancer function

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

The Preprocess_MAdata_Cancer function

Description

Internal. Pre-process gene expression data for cancer samples.

Usage

Preprocess_MAdata_Cancer(
  CancerSite,
  Directory,
  File,
  MissingValueThresholdGene = 0.3,
  MissingValueThresholdSample = 0.1,
  doBatchCorrection,
  batch.correction.method,
  BatchData
)

Arguments

CancerSite	TCGA code for the cancer site.
Directory	Directory.
File	File.
MissingValueThresholdGene	threshold for missing values per gene. Genes with a percentage of NAs greater than this threshold are removed. Default is 0.3.
MissingValueThresholdSample	threshold for missing values per sample. Samples with a percentage of NAs greater than this threshold are removed. Default is 0.1.

Value

The data matrix.

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