getDataClustering {PhyloProfile} | R Documentation

## Get data for calculating distance matrix from phylogenetic profiles

### Description

Get data for calculating distance matrix from phylogenetic profiles

### Usage

    getDataClustering(data, profileType = "binary", var1AggBy = "max",
        var2AggBy = "max")

### Arguments

`data` | a data frame contains processed and filtered profiles (see ?fullProcessedProfile and ?filterProfileData, ?fromInputToProfile)
`profileType` | type of data used for calculating the distance matrix. Either "binary" (consider only the presence/absence status of orthlogs), or "var1"/"var2" for taking values of the additional variables into account. Default = "binary".
`var1AggBy` | aggregate method for VAR1 (min, max, mean or median). Default = "max".
`var2AggBy` | aggregate method for VAR2 (min, max, mean or median). Default = "max".

### Value

A wide dataframe contains values for calculating distance matrix.

### Author(s)

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

### See Also

`fromInputToProfile`

### Examples

    data("superTaxonProfile", package="PhyloProfile")
    data <- superTaxonProfile
    profileType <- "binary"
    var1AggregateBy <- "max"
    var2AggregateBy <- "mean"
    getDataClustering(data, profileType, var1AggregateBy, var2AggregateBy)

[Package PhyloProfile version 1.4.11 Index]