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

ClustDistList-class

R Documentation

Storing multiple ClustDist instances

Description

A class for storing lists of ClustDist instances.

Objects from the Class

Object of this class are created with the clustDist function.

Slots

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.

Methods

"[[": 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.

Author(s)

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

Examples


  library(pRolocdata)
  data(dunkley2006)

  ## Convert annotation data e.g. markers, to a matrix e.g. MM
  xx <- mrkVecToMat(dunkley2006, vfcol = "markers", mfcol = "MM")
  
  ## get distances for protein sets 
  dd <- clustDist(xx, fcol = "MM", k = 1:3)

  ## filter
  xx <- filterMinMarkers(xx, n = 50, fcol = "MM")
  xx <- filterMaxMarkers(xx, p = .25, fcol = "MM")
  
  ## get distances for protein sets
  dd <- clustDist(xx, fcol = "MM")

  ## plot distances for all protein sets
  plot(dd)

  names(dd)

  ## Extract a sub-list of ClustDist objects
  dd[1]

  ## Extract 1st ClustDist object
  dd[[1]]

lgatto/pRoloc documentation built on June 14, 2025, 7:56 p.m.