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

Source: R/YARN.R
checkMisAnnotation.Rd

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')