Storing multiple ClustDist instances

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

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

Examples

  library('pRolocdata')
  data(dunkley2006)
  par <- setAnnotationParams(inputs =
                    c("Arabidopsis thaliana genes",
                    "Gene stable ID"))
#> Using species Arabidopsis thaliana genes (TAIR10)
#> Warning: Ensembl will soon enforce the use of https.
#> Ensure the 'host' argument includes "https://"
#> Using feature type Gene stable ID(s) [e.g. AT1G01010]
#> Connecting to Biomart...
#> Warning: Ensembl will soon enforce the use of https.
#> Ensure the 'host' argument includes "https://"
                    
  ## add protein set/annotation information                  
  xx <- addGoAnnotations(dunkley2006, par)
  
  ## filter
  xx <- filterMinMarkers(xx, n = 50)
#> Retaining 18 out of 165 in GOAnnotations
  xx <- filterMaxMarkers(xx, p = .25)
#> Retaining 14 out of 18 in GOAnnotations
  
  ## get distances for protein sets
  dd <- clustDist(xx)
#> 
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  ## plot distances for all protein sets 
  plot(dd)

  
  names(dd)
#>  [1] "mitochondrion"                  "plant-type vacuole"            
#>  [3] "nucleus"                        "vacuole"                       
#>  [5] "plasmodesma"                    "cytosol"                       
#>  [7] "chloroplast"                    "plastid"                       
#>  [9] "endoplasmic reticulum membrane" "cytoplasm"                     
#> [11] "Golgi membrane"                 "endosome"                      
#> [13] "chloroplast envelope"           "trans-Golgi network"           
  
  ## Extract first 4 ClustDist objects of the ClustDistList
  dd[1:4]
#> Instance of class 'ClustDistList' containig 4 objects.
  
  ## Extract 1st ClustDist object
  dd[[1]]
#> Object of class "ClustDist"
#> fcol =  GOAnnotations 
#>  term =  GO:0005739 
#>  id =  mitochondrion 
#>  nrow =  160 
#> k's tested: 1 2 3 4 5 
#>   Size:  160 
#>   Size:  106 
#>   Size:  106 
#>   Size:  80 
#>   Size:  74 
#> Clusters info:
#>       ks.mean    mean ks.norm     norm
#> k = 1       1  0.4410       1  0.08123
#> k = 2       1  0.1844       1  0.03896
#> k = 3       1  0.1844       1  0.03896
#> k = 4       1  0.1515       1  0.03517
#> k = 5       1 *0.1270       1 *0.03026