checkMisAnnotation: Check for wrong annotation of a sample using classical MDS...

In QuackenbushLab/yarn: YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization

Check for wrong annotation of a sample using classical MDS and control genes.

Description

Check for wrong annotation of a sample using classical MDS and control genes.

Usage

checkMisAnnotation(obj, phenotype, controlGenes = "all",
  columnID = "chromosome_name", plotFlag = TRUE, legendPosition = NULL,
  ...)

Arguments

obj	ExpressionSet object.
phenotype	phenotype column name in the phenoData slot to check.
controlGenes	Name of controlGenes, ie. 'Y' chromosome. Can specify 'all'.
columnID	Column name where controlGenes is defined in the featureData slot if other than 'all'.
plotFlag	TRUE/FALSE Whether to plot or not
legendPosition	Location for the legend.
...	Extra parameters for plotCMDS function.

Value

Plots a classical multi-dimensional scaling of the 'controlGenes'. Optionally returns co-ordinates.

Examples

data(bladder)
checkMisAnnotation(bladder,'GENDER',controlGenes='Y',legendPosition='topleft')

QuackenbushLab/yarn documentation built on March 7, 2024, 3:53 p.m.