Preprocess_GeneExpression {MethylMix} | R Documentation

## The Preprocess_GeneExpression function

### Description

Pre-processes gene expression data from TCGA.

### Usage

    Preprocess_GeneExpression(CancerSite, MAdirectories,
      MissingValueThresholdGene = 0.3, MissingValueThresholdSample = 0.1)

### Arguments

`CancerSite` | character of length 1 with TCGA cancer code.
`MAdirectories` | character vector with directories with the downloaded data. It can be the object returned by the Download_DNAmethylation function.
`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.

### Details

Pre-process includes eliminating samples and genes with too many NAs, imputing NAs, and doing Batch correction.

### Value

List with the pre-processed data matrix for cancer and normal samples.

### Examples

    ## Not run:

    # Optional register cluster to run in parallel
    library(doParallel)
    cl <- makeCluster(5)
    registerDoParallel(cl)

    # Gene expression data for ovarian cancer
    cancerSite <- "OV"
    targetDirectory <- paste0(getwd(), "/")

    # Downloading gene expression data
    GEdirectories <- Download_GeneExpression(cancerSite, targetDirectory, TRUE)

    # Processing gene expression data
    GEProcessedData <- Preprocess_GeneExpression(cancerSite, GEdirectories)

    # Saving gene expression processed data
    saveRDS(GEProcessedData, file = paste0(targetDirectory, "GE_", cancerSite, "_Processed.rds"))

    stopCluster(cl)

    ## End(Not run)

[Package MethylMix version 2.20.0 Index]