cluster.pathways: Clustering of Pathways

In SOMMD: Self Organising Maps for the Analysis of Molecular Dynamics Data

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"
)

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

Value

representatives a vector of frames representatives of each neuron

Author(s)

Stefano [e-mail]

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")

SOMMD documentation built on Oct. 2, 2024, 5:07 p.m.