checkMisAnnotation {yarn} | R Documentation |
Check for wrong annotation of a sample using classical MDS and control genes.
checkMisAnnotation(obj, phenotype, controlGenes = "all", columnID = "chromosome_name", plotFlag = TRUE, legendPosition = NULL, ...)
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 |
Plots a classical multi-dimensional scaling of the 'controlGenes'. Optionally returns co-ordinates.
data(bladder) checkMisAnnotation(bladder,'GENDER',controlGenes='Y',legendPosition='topleft')