getDistanceMatrix: Calculate the distance matrix

In PhyloProfile: PhyloProfile

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 ([e-mail]), Vinh Tran ([e-mail])

See Also

getDataClustering

Examples

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

Example output

             100136at6656 100265at6656 101621at6656
100265at6656    0.1282320                          
101621at6656    0.1911148    0.1274281             
103479at6656    0.1710216    0.1042150    0.0000000

PhyloProfile documentation built on March 27, 2021, 6:01 p.m.