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

In BIONF/PhyloProfile: PhyloProfile

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), "orthoID" (consider ortholog IDs as values for clustering), "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("finalProcessedProfile", package="PhyloProfile")
data <- finalProcessedProfile
profileType <- "binary"
var1AggregateBy <- "max"
var2AggregateBy <- "mean"
getDataClustering(data, profileType, var1AggregateBy, var2AggregateBy)

BIONF/PhyloProfile documentation built on Dec. 23, 2024, 4:23 a.m.