getDataClustering {PhyloProfile} | R Documentation |
Get data for calculating distance matrix from phylogenetic profiles
getDataClustering(data, profileType = "binary", var1AggBy = "max", var2AggBy = "max")
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". |
A wide dataframe contains values for calculating distance matrix.
Carla Mölbert (carla.moelbert@gmx.de), Vinh Tran (tran@bio.uni-frankfurt.de)
data("superTaxonProfile", package="PhyloProfile") data <- superTaxonProfile profileType <- "binary" var1AggregateBy <- "max" var2AggregateBy <- "mean" getDataClustering(data, profileType, var1AggregateBy, var2AggregateBy)