getSilhouetteStats: Draw silhouette plots and get silhouette statistics

In jsemple19/EMclassifieR: Classify DSMF data using the Expectation Maximisation algorithm

Draw silhouette plots and get silhouette statistics

Description

Draw silhouette plots and get silhouette statistics

Usage

getSilhouetteStats(
  dataOrderedByClass,
  numClasses,
  outFileBase,
  outPath,
  EMrep = NULL,
  doIndividualPlots = FALSE,
  silStats = NULL,
  distMetric = list(name = "euclidean", rescale = F)
)

Arguments

dataOrderedByClass	A matrix of methylation or bincount values (reads x position) that have been ordered by class. The assigned class, e.g. "__class1" etc has been appended to read names.
numClasses	An integer indicating the number of classes to learn
outFileBase	A string that will be used in the filenames and titles of the plots produced
outPath	path to directory where plots will be saved
EMrep	An integer indicating which EM repeat this is
doIndividualPlots	Produce individual plots for each repeat (default=F)
silStats	data.frame with statistics about the silhouette plots (default=NULL)
distMetric	A list with the name of the distance metric and any parameters it might require

Value

silStats data.frame with statistics about the silhouette plots

jsemple19/EMclassifieR documentation built on Aug. 12, 2022, 2:57 p.m.