Methods for dealing with control data for Illumina methylation data — qcplot • methylumi

The `qcplot` function simply generates a plot of the control probe information for a given `controlType`.

Usage

qcplot(object,controltype,...)
controlTypes(object,...)

Arguments

object: An object of class [MethyLumiSet-class] or [MethyLumiQC-class].
controltype: A single character value representing the bead type to plot from the quality control data. The available types are accessible via the `controlTypes` method.
...: Passed to the plot function.

Details

The descriptions of the various control types can be obtained from the Illumina methylation user's guides.

See also

[MethyLumiSet-class], [MethyLumiQC-class]

Author

Sean Davis <seandavi@gmail.com>

Examples

data(mldat)
controlTypes(mldat)
#> [1] "ALLELE SPECIFIC EXTENSION" "EXTENSION GAP"            
#> [3] "FIRST HYBRIDIZATION"       "GENDER"                   
#> [5] "NEGATIVE"                  "PCR CONTAMINATION"        
#> [7] "SECOND HYBRIDIZATION"     
qcplot(mldat, controlTypes(mldat)[3])