View source: R/clusterProfile.R
getDataClustering | 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), "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". |
A wide dataframe contains values for calculating distance matrix.
Carla Mölbert (carla.moelbert@gmx.de), Vinh Tran (tran@bio.uni-frankfurt.de)
fromInputToProfile
data("finalProcessedProfile", package="PhyloProfile")
data <- finalProcessedProfile
profileType <- "binary"
var1AggregateBy <- "max"
var2AggregateBy <- "mean"
getDataClustering(data, profileType, var1AggregateBy, var2AggregateBy)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.