DEGsExtraction {KnowSeq} | R Documentation

## DEGsExtraction performs the analysis to extract the Differentially Expressed Genes (DEGs) among the classes to compare.

### Description

The function performs the analysis to extract the Differentially Expressed Genes (DEGs) among the classes to compare. The number of final DEGs can change depending on the p-value and the LFC indicated by parameters of the function. Furthermore, the function detects if the number of classes are greater than 2 to perform a multiclass DEGs analysis.

### Usage

    DEGsExtraction(
      expressionMatrix,
      labels,
      pvalue = 0.05,
      lfc = 1,
      cov = 1,
      nmax = 1,
      multiDegsMethod = "cov",
      number = Inf,
      CV = FALSE,
      numFolds = 5
    )

### Arguments

`expressionMatrix` | The expressionMatrix parameter is an expression matrix or data.frame that contains the genes in the rows and the samples in the columns.
`labels` | A vector or factors that contains the labels for each of the samples in the expressionMatrix parameter.
`pvalue` | The value of the p-value which determines the DEGs. If one or more genes have a p-value lower or equal to the selected p-value, they would be considered as DEGs.
`lfc` | The value of the LFC which determines the DEGs. If one or more genes have a LFC greater or equal to the selected LFC, they would be considered as DEGs.
`cov` | This value only works when there are more than two classes in the labels. This parameter establishes a minimum number of pair of classes combination in which exists differential expression to consider a genes as expressed genes.
`nmax` | This value only works when there are more than two classes in the labels. NMAX indicates the maximum number of DEGs selected for each class pair comparison.
`multiDegsMethod` | Select the multiclass extraction method for the process: cov or nmax
`number` | The maximum number of desired genes as output of limma. As default, the function returns all the extracted DEGs with the selected parameters.
`CV` | A boolean value that has to be setted to TRUE if the user would to run a Cross-Validation DEGs extraction process.
`numFolds` | This parameter indicates the number of folds for the Cross-Validation process.

### Value

A list that contains two objects. The table with statistics of the different DEGs and a reduced expression matrix which contains the DEGs and the samples.

### Examples

    dir <- system.file("extdata", package="KnowSeq")
    load(paste(dir,"/expressionExample.RData",sep = ""))

    expressionMatrix <- calculateGeneExpressionValues(countsMatrix,myAnnotation, genesNames = TRUE)

    DEGsInformation <- DEGsExtraction(expressionMatrix, labels, lfc = 2.0,
    pvalue = 0.01, number = Inf)

    topTable <- DEGsInformation$Table

    DEGsMatrix <- DEGsInformation$DEGsMatrix

[Package KnowSeq version 1.8.1 Index]