getDataClustering: Get data for calculating distance matrix from phylogenetic...

In PhyloProfile: PhyloProfile

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

See Also

fromInputToProfile

Examples

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

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