clustDist {pRoloc} | R Documentation

## Pairwise Distance Computation for Protein Information Sets

### Description

This function computes the mean (normalised) pairwise distances for pre-defined sets of proteins.

### Usage

    clustDist(object, k = 1:5, fcol = "GOAnnotations", n = 5,
      verbose = TRUE, seed)

### Arguments

`object` | An instance of class `"MSnSet"`.
`k` | The number of clusters to try fitting to the protein set. Default is `k = 1:5`.
`fcol` | The feature meta-data containing matrix of protein sets/ marker definitions. Default is `GOAnnotations`.
`n` | The minimum number of proteins per set. If protein sets contain less than `n` instances they will be ignored. Defualt is 5.
`verbose` | A logical defining whether a progress bar is displayed.
`seed` | An optional seed for the random number generator.

### Details

The input to the function is a `MSnSet` dataset containing a matrix appended to the feature data slot identifying the membership of protein instances to a pre-defined set(s) e.g. a specific Gene Ontology term etc.

For each protein set, the `clustDist` function (i) extracts all instances belonging to the set, (ii) using the `kmeans` algorithm fits and tests `k = c(1:5)` (default) cluster components to each set, (iii) calculates the mean pairwise distance for each `k` tested.

Note: currently distances are calcualted in Euclidean space, but other distance metrics will be supported in the future).

The output is a `list` of `ClustDist` objects, one per information cluster. The `ClustDist` class summarises the algorithm information such as the number of k's tested for the kmeans, and mean and normalised pairwise Euclidean distances per numer of component clusters tested. See `?ClustDist` for more details.

### Value

An instance of `"ClustDistList"` containing a `"ClustDist"` instance for every protein set, which summarises the algorithm information such as the number of k's tested for the kmeans, and mean and normalised pairwise Euclidean distances per numer of component clusters tested.

### Author(s)

Lisa Breckels

### See Also

For class definitions see `"ClustDistList"` and `"ClustDist"`.

### Examples

    library(pRolocdata)
    data(dunkley2006)
    par <- setAnnotationParams(inputs =
                       c("Arabidopsis thaliana genes",
                       "Gene stable ID"))
    ## add protein sets/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 clusters for first 'ClustDist' object
    ## in the 'ClustDistList'
    plot(dd[[1]], xx)
    ## plot distances for all protein sets
    plot(dd)
    ## Extract normalised distances
    ## Normalise by n^1/3
    minDist <- getNormDist(dd, p = 1/3)
    ## Get new order according to lowest distance
    o <- order(minDist)
    ## Re-order GOAnnotations
    fData(xx)$GOAnnotations <- fData(xx)$GOAnnotations[, o]
    if (interactive()) {
    pRolocVis(xx, fcol = "GOAnnotations")
    }

[Package pRoloc version 1.34.0 Index]