getDistanceMatrix {PhyloProfile} | R Documentation

## Calculate the distance matrix

### Description

Calculate the distance matrix

### Usage

    getDistanceMatrix(profiles = NULL, method = "mutualInformation")

### Arguments

`profiles` | dataframe contains profile data for distance calculating (see ?getDataClustering)
`method` | distance calculation method ("euclidean", "maximum", "manhattan", "canberra", "binary", "distanceCorrelation", "mutualInformation" or "pearson" for binary data; "distanceCorrelation" or "mutualInformation" for non-binary data). Default = "mutualInformation".

### Value

A calculated distance matrix for input phylogenetic profiles.

### Author(s)

Carla Mölbert (carla.moelbert@gmx.de), Vinh Tran (tran@bio.uni-frankfurt.de)

### See Also

`getDataClustering`

### Examples

    data("finalProcessedProfile", package="PhyloProfile")
    data <- finalProcessedProfile
    profileType <- "binary"
    profiles <- getDataClustering(
        data, profileType, var1AggregateBy, var2AggregateBy)
    method <- "mutualInformation"
    getDistanceMatrix(profiles, method)

[Package PhyloProfile version 1.2.8 Index]