pRoloc (version 1.12.3)

ClustDist-class: Class "ClustDist"

Description

The ClustDist summaries algorithm information, from running the clustDist function, such as the number of k's tested for the kmeans, and mean and normalised pairwise (Euclidean) distances per numer of component clusters tested.

Objects from the Class

Object of this class are created with the clustDist function.

Examples

showClass("ClustDist")
  
  library('pRolocdata')
  data(dunkley2006)
  par <- setAnnotationParams(inputs =
                    c("Arabidopsis thaliana genes",
                    "TAIR locus ID"))
                    
  ## add protein set/annotation information                  
  xx <- addGoAnnotations(dunkley2006, par)
  
  ## filter
  xx <- filterMinMarkers(xx, n = 50)
  xx <- filterMaxMarkers(xx, p = .25)
  
  ## get distances for protein sets
  dd <- clustDist(xx)
  
  ## plot clusters for first 'ClustDist' object 
  ## in the 'ClustDistList'
  plot(dd[[1]], xx)
  
  ## plot distances for all protein sets 
  plot(dd)