checkMisAnnotation {yarn} | R Documentation

## 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')

[Package yarn version 1.16.0 Index]