ClustDistList-class: Storing multiple ClustDist instances
In pRoloc: A unifying bioinformatics framework for spatial proteomics

Description Objects from the Class Slots Methods Author(s) Examples

A class for storing lists of ClustDist instances.

Object of this class are created with the clustDist function.

x:: Object of class list containing valid ClustDist instances.
log:: Object of class list containing an object creation log, containing among other elements the call that generated the object.
.__classVersion__:: The version of the instance. For development purposes only.

"[[": Extracts a single ClustDist at position.
"[": Extracts one of more ClustDists as ClustDistList.
length: Returns the number of ClustDists.
names: Returns the names of ClustDists, if available. The replacement method is also available.
show: Display the object by printing a short summary.
lapply(x, FUN, ...): Apply function FUN to each element of the input x. If the application of FUN returns and ClustDist, then the return value is an ClustDistList, otherwise a list

plot: Plots a boxplot of the distance results per protein set.

Lisa M Breckels <lms79@cam.ac.uk>

  library('pRolocdata')
  data(dunkley2006)
  par <- setAnnotationParams(inputs =
                    c("Arabidopsis thaliana genes",
                    "Gene stable 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 distances for all protein sets 
  plot(dd)
  
  names(dd)
  
  ## Extract first 4 ClustDist objects of the ClustDistList
  dd[1:4]
  
  ## Extract 1st ClustDist object
  dd[[1]]