RnBeads (version 1.4.0)

rnb.plot.marker.fstat: rnb.plot.marker.fstat

Description

Plot the the cell type marker selection based on the reference methylome data

Usage

rnb.plot.marker.fstat(ct.object, writeToFile = FALSE, ...)

Arguments

ct.object

Object of class CellTypeInferenceResult as returned by rnb.execute.ct.estimation.

writeToFile

If TRUE, the plot will be written to a file.

...

Other arguments to createReportPlot.

Value

if writeToFile=TRUE an object of class ReportPlot, and the plotted reordered F-statistics vector otherwise

Details

The F-statistic values from the cell type association model (first part of eqn. (1) in [1]) are plotted in decreasing order for all tested CpG positions. A vertical line gives a cut-off for the number of selected cell type markers.

References

1. Houseman, Eugene and Accomando, William and Koestler, Devin and Christensen, Brock and Marsit, Carmen and Nelson, Heather and Wiencke, John and Kelsey, Karl. DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics 2012, 13:86