RNAseqQA: RNAseqQA performs the quality analysis of an expression...

In CasedUgr/KnowSeq: KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

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)

CasedUgr/KnowSeq documentation built on Aug. 16, 2022, 6:19 a.m.