ClustDistList-class: Storing multiple ClustDist instances

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

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

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  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]]


pRoloc documentation built on May 20, 2017, 10:26 p.m.
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