TCGA_Preprocess_GeneExpression: The TCGA_Preprocess_GeneExpression function

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

The TCGA_Preprocess_GeneExpression function

Description

Pre-processes gene expression data from TCGA.

Usage

TCGA_Preprocess_GeneExpression(
  CancerSite,
  MAdirectories,
  mode = "Regular",
  doBatchCorrection = FALSE,
  batch.correction.method = "Seurat",
  MissingValueThresholdGene = 0.3,
  MissingValueThresholdSample = 0.1,
  cores = 1
)

Arguments

CancerSite	character string indicating the TCGA cancer code.
MAdirectories	character vector with directories with the downloaded data. It can be the object returned by the GEO_Download_GeneExpression function.
mode	character string indicating whether the genes in the gene expression data are miRNAs or lncRNAs. Should be either 'Regular', 'Enhancer', 'miRNA' or 'lncRNA'. This value should be consistent with the same parameter in the TCGA_Download_GeneExpression function. Default: 'Regular'.
doBatchCorrection	logical indicating whether to perform batch effect 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'. Seurat is much fatster than the Combat.
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.
cores	integer indicating the number of cores to be used for performing batch correction with Combat

Details

Pre-process includes eliminating samples and genes with too many NAs, imputing NAs, and doing Batch correction. If the rownames of the gene expression data are ensembl ENSG names or ENST names, the function will convert them to the human gene symbol (HGNC).

Value

pre-processed gene expression data matrix.

Examples

# Example #1: Preprocessing gene expression for Regular mode

 GEdirectories <- TCGA_Download_GeneExpression(CancerSite = 'OV',
                                               TargetDirectory = tempdir())
 GEProcessedData <- TCGA_Preprocess_GeneExpression(CancerSite = 'OV',
                                                   MAdirectories = GEdirectories)

# Example #2: Preprocessing gene expression for miRNA mode

 GEdirectories <- TCGA_Download_GeneExpression(CancerSite = 'OV',
                                               TargetDirectory = tempdir(),
                                               mode = 'miRNA')

 GEProcessedData <- TCGA_Preprocess_GeneExpression(CancerSite = 'OV',
                                                   MAdirectories = GEdirectories,
                                                   mode = 'miRNA')

# Example #3: Preprocessing gene expression for lncRNA mode

 GEdirectories <- TCGA_Download_GeneExpression(CancerSite = 'OV',
                                               TargetDirectory = tempdir(),
                                               mode = 'lncRNA')

 GEProcessedData <- TCGA_Preprocess_GeneExpression(CancerSite = 'OV',
                                                   MAdirectories = GEdirectories,
                                                   mode = 'lncRNA')

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