cluster_ID: cluster_ID

In Fiscore: Effective Protein Structural Data Visualisation and Exploration

Description

Function to select an optimal number of clusters and a model to be fitted during the EM phase of clustering for Gaussian Mixture Models. The function provides summaries and helps to visualise clusters based on Fi-score using scatter plotting and dimension reduction plots.

Usage

cluster_ID(
  pdb_df,
  max_range = 20,
  secondary_structures = TRUE,
  clusters = NULL,
  modelNames = NULL
)

Arguments

pdb_df	data frame containing processed PDB file with Fi-score values
max_range	number of clusters to consider during model selection; default 20 clusters
secondary_structures	include information on secondary structure elements from PDB when plotting, default value is TRUE
clusters	number of clusters to test not based on the best BIC output, user also needs to supply modelNames
modelNames	can only be supplied when clusters are also specified, this option will model based on the user parameters

Value

A data frame object that contains a summary of clusters

Examples

path_to_processed_PDB<- system.file("extdata", "pdb_df.tabular", package="Fiscore")
# basic usage of cluster_ID
pdb_df<-read.table(path_to_processed_PDB)
head(cluster_ID(pdb_df))

Fiscore documentation built on Sept. 5, 2021, 5:51 p.m.