ClustDistList-class {pRoloc} | 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)
      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]]

[Package pRoloc version 1.28.0 Index]