RNAseqQA {KnowSeq} | R Documentation

## RNAseqQA performs the quality analysis of an expression matrix.

### Description

RNAseqQA performs the quality analysis of an expression matrix. This function generates different plots over expression data in order to detect possible outliers.

### Usage

    RNAseqQA(
      expressionMatrix,
      outdir = "SamplesQualityAnalysis",
      toPNG = TRUE,
      toPDF = TRUE,
      toRemoval = FALSE
    )

### Arguments

`expressionMatrix` | A matrix that contains the gene expression values.
`outdir` | The output directory to store the report of arrayQualityMetrics
`toPNG` | Boolean variable to indicate if a plot would be save to PNG.
`toPDF` | Boolean variable to indicate if a plot would be save to PDF.
`toRemoval` | Boolean variable to indicate if detected outliers will be removed from original data

### Value

A list containing found outliers for each realized test or corrected data if toRemoval is TRUE.

### Examples

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

[Package KnowSeq version 1.1.27 Index]