SOMMD (version 0.1.2)

cluster.pathways: Clustering of Pathways

Description

Cluster pathways according to a time dependent or independent scheme

Usage

cluster.pathways(
  SOM,
  start,
  end,
  time.dep = "independent",
  method = "complete"
)

Value

representatives a vector of frames representatives of each neuron

Arguments

SOM

a kohonen SOM object.

start

the vector specifying the starting frame of each replicas

end

the vector specifying the ending frame of each replicas

time.dep

choose whether to use time "dependent" or "independent" clustering of pathways

method

the method to be passed to hclust for the clustering

Author

Stefano Motta

Examples

#Read trajectory
trj <- read.trj(trjfile = system.file("extdata", "HIF2a-MD.xtc", package = "SOMMD"),
  topfile = system.file("extdata", "HIF2a.gro", package = "SOMMD"))
#Assign length of the replicas
trj$start <- seq(1, 25, by=5)
trj$end <- seq(5, 25, by=5)
#Read example SOM data
som_model <- readRDS(system.file("extdata", "SOM_HIFa.rds", package = "SOMMD"))
#Cluster Pathways using the time dependent algorithm
clus.paths.tdep <- cluster.pathways(som_model, start=trj$start, end=trj$end,
  time.dep="dependent")
#Cluster Pathways using the time independent algorithm
clus.paths.tindep <- cluster.pathways(som_model,
  start=trj$start, end=trj$end, time.dep="independent")