domainDist {chroGPS} | R Documentation

## Overview of intra and inter-domain distances.

### Description

Given a distance of pairwise distances or dissimilarities between elements, return intra and inter-group sets of distances based on a given group definition. This is useful to get an insight on domain robustness for functional related genes or factors.

### Usage

    domainDist(d, gps='factors', domain, type='intra', col='white', avg=FALSE,
    plot=TRUE, ...)

### Arguments

`d` | Distance/Dissimilarities matrix, usually the slot `d` on a `distGPS` object, but any distance matrix can be given as input.
`gps` | 'factors' for a chroGPS-factors distance matrix, 'genes' for a chroGPS-genes one.
`domain` | Character vector with group identity for each element `d`. It can be a functional domain classification (i.e. 'Activation', 'Repression', etc), given for each factor on a chroGPS-factors map or for each gene in a chroGPS-genes map. However, any classification of interest can be used (pathways, gene ontology, etc.)
`type` | Intradomain ('intra') or Interdomain ('inter') distance overview.
`col` | Character vector with colors to be passed to `plot`.
`avg` | TRUE to return also the average inter or intra domain distance.
`plot` | TRUE to generate inter/intra domain boxplots.
`...` | Additional parameters given to the generic function `plot`.

### Value

List of inter or intra domain distances.

### Examples

    # Not run
    # data(s2)
    # d <- distGPS(s2,metric='avgdist',mc.cores=1)
    # d.intra <- domainDist(as.matrix(d),domain=s2names$Color,type='intra',plot=TRUE)
    # d.inter <- domainDist(as.matrix(d),domain=s2names$Color,type='inter',plot=TRUE)

[Package chroGPS version 1.28.0 Index]