TCGAanalyze_DEA {TCGAbiolinks} | R Documentation

## Differential expression analysis (DEA) using edgeR or limma package.

### Description

TCGAanalyze_DEA allows user to perform Differentially expression analysis (DEA), using edgeR package or limma to identify differentially expressed genes (DEGs). It is possible to do a two-class analysis.

TCGAanalyze_DEA performs DEA using following functions from edgeR:

1. edgeR::DGEList converts the count matrix into an edgeR object.

2. edgeR::estimateCommonDisp each gene gets assigned the same dispersion estimate.

3. edgeR::exactTest performs pair-wise tests for differential expression between two groups.

4. edgeR::topTags takes the output from exactTest(), adjusts the raw p-values using the False Discovery Rate (FDR) correction, and returns the top differentially expressed genes.

TCGAanalyze_DEA performs DEA using following functions from limma:

1. limma::makeContrasts construct matrix of custom contrasts.

2. limma::lmFit Fit linear model for each gene given a series of arrays.

3. limma::contrasts.fit Given a linear model fit to microarray data, compute estimated coefficients and standard errors for a given set of contrasts.

4. limma::eBayes Given a microarray linear model fit, compute moderated t-statistics, moderated F-statistic, and log-odds of differential expression by empirical Bayes moderation of the standard errors towards a common value.

5. limma::toptable Extract a table of the top-ranked genes from a linear model fit.

### Usage

    TCGAanalyze_DEA(mat1, mat2, metadata = TRUE, Cond1type, Cond2type,
      pipeline = "edgeR", method = "exactTest", fdr.cut = 1,
      logFC.cut = 0, elementsRatio = 30000, batch.factors = NULL,
      ClinicalDF = data.frame(), paired = FALSE, log.trans = FALSE,
      voom = FALSE, trend = FALSE, MAT = data.frame(),
      contrast.formula = "", Condtypes = c())

### Arguments

`mat1` | numeric matrix, each row represents a gene, each column represents a sample with Cond1type
`mat2` | numeric matrix, each row represents a gene, each column represents a sample with Cond2type
`metadata` | Add metadata
`Cond1type` | a string containing the class label of the samples in mat1 (e.g., control group)
`Cond2type` | a string containing the class label of the samples in mat2 (e.g., case group)
`pipeline` | a string to specify which package to use ("limma" or "edgeR")
`method` | is 'glmLRT' (1) or 'exactTest' (2) used for edgeR (1) Fit a negative binomial generalized log-linear model to the read counts for each gene (2) Compute genewise exact tests for differences in the means between two groups of negative-binomially distributed counts.
`fdr.cut` | is a threshold to filter DEGs according their p-value corrected
`logFC.cut` | is a threshold to filter DEGs according their logFC
`elementsRatio` | is number of elements processed for second for time consumation estimation
`batch.factors` | a vector containing strings to specify options for batch correction. Options are "Plate", "TSS", "Year", "Portion", "Center", and "Patients"
`ClinicalDF` | a dataframe returned by GDCquery_clinic() to be used to extract year data
`paired` | boolean to account for paired or non-paired samples. Set to TRUE for paired case
`log.trans` | boolean to perform log cpm transformation. Set to TRUE for log transformation
`voom` | boolean to perform voom transformation for limma-voom pipeline. Set to TRUE for voom transformation
`trend` | boolean to perform limma-trend pipeline. Set to TRUE to go through limma-trend
`MAT` | matrix containing expression set as all samples in columns and genes as rows. Do not provide if mat1 and mat2 are used
`contrast.formula` | string input to determine coefficients and to design contrasts in a customized way
`Condtypes` | vector of grouping for samples in MAT

### Value

table with DEGs containing for each gene logFC, logCPM, pValue,and FDR, also for each contrast

### Examples

    dataNorm <- TCGAbiolinks::TCGAanalyze_Normalization(dataBRCA, geneInfo)
    dataFilt <- TCGAanalyze_Filtering(tabDF = dataBRCA, method = "quantile", qnt.cut =  0.25)
    samplesNT <- TCGAquery_SampleTypes(colnames(dataFilt), typesample = c("NT"))
    samplesTP <- TCGAquery_SampleTypes(colnames(dataFilt), typesample = c("TP"))
    dataDEGs <- TCGAanalyze_DEA(mat1 = dataFilt[,samplesNT],
                                mat2 = dataFilt[,samplesTP],
                                Cond1type = "Normal",
                                Cond2type = "Tumor")

[Package TCGAbiolinks version 2.12.6 Index]