QC_expressionset: Quality Control procedures for expression data

In frankRuehle/systemsbio: Streamlined Analysis and Integration of Systems Biology Data

Description

Application of diverse quality control metrix for gene expression data.

Usage

QC_expressionset(
  eset,
  projectfolder = "GEX/QC",
  projectname = NULL,
  groupColumn = "Sample_Group",
  phDendro = "Sample_Group",
  flashClustMethod = "average",
  cex.dendroLabels = 0.6,
  figure.res = 300,
  threshold.Z.k = -5
)

Arguments

eset	ExpressionSet or ExpressionSetIllumina object
projectfolder	character vector with name of desired output folder (will be generated if not exisiting).
projectname	character vector containing prefix for names of output files.
groupColumn	character vector with name of group column in phenotype data.
phDendro	character vector with phenotypes of eset to be displayed in sample dendrogram.
flashClustMethod	character vector with the agglomeration method to be used in WGCNA package. Can be one of "ward", "single", "complete", "average", "mcquitty", "median" or "centroid".
cex.dendroLabels	numeric. Controls size of labels sample in dendrogram.
figure.res	numeric resolution for png.
threshold.Z.k	numeric. Threshold for outlier prediction WGCNA package (outlier samples are highlighted in red in sample dendrogram).

Details

Function implements several approaches for quality control of expression data, which are stored in a newly generated 'project folder. - Illumina internal control plots, box-plots and MA-plots (if applicable). - Quality control as implemented in the arrayQualityMetrics-package (subfolder 'quality_metrics') - Quality control routines implemented in WGCNA-package. This comprises a sample dendrogram with included outlier prediction as well as boolean vectors for sample and gene quality calculated by the goodSamplesGenes-function.

Value

The returned value is a list of 3 - goodGenes: boolean vector indicating genes passing QC-criteria as implemented in WGCNA. - goodSamples: boolean vector indicating samples passing QC-criteria as implemented in WGCNA. - allOK: boolean. If TRUE all samples and all genes pass QC-criteria as implemented in WGCNA. Several plots and files are generated as side-effects and stored in the project folder.

Author(s)

Frank Ruehle

frankRuehle/systemsbio documentation built on Sept. 14, 2020, 1:18 a.m.