TMixClust: Clusters the time series data in a given number of groups

In cbg-ethz/TMixClust: Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines

Description

TMixClust is the central function of the package. It clusters the given time series data into a specified number of clusters.

Usage

TMixClust(time_series_df, time_points = seq_len(ncol(time_series_df)),
  nb_clusters = 2, em_iter_max = 1000, mc_em_iter_max = 10,
  em_ll_convergence = 0.001)

Arguments

time_series_df	data frame containing the time series. Each row is a time series comprised of the time series name which is also the row name, and the time series values at each time point.
time_points	vector containing numeric values for the time points. Default: seq_len(ncol(time_series_df)).
nb_clusters	desired number of clusters
em_iter_max	maximum number of iterations for the expectation-maximization (EM) algorithm. Default: 1000.
mc_em_iter_max	maximum number of iterations for Monte-Carlo resampling. Default is 100.
em_ll_convergence	convergence threshold for likelihood improvement. Default is 0.001.

Value

list object with the following attributes:

• em_gss_obj_list object of class gss containing estimated parameters of the mixed-effects model (see package vignette for more details).

• em_pi_k vector containing the mixing coefficients corresponding to each cluster

• em_mat_post matrix containing the posterior values for each time series and cluster

• em_cluster_assignment vector with the clustering attribution for each time series

• el_ll vector containing the log likelihood values at each iteration in the EM algorithm

• ts_data the same as the input time series data-frame

• ts_time_points the same as the input time-points vector

Author(s)

Monica Golumbeanu, [e-mail]

References

Golumbeanu M, Desfarges S, Hernandez C, Quadroni M, Rato S, Mohammadi P, Telenti A, Beerenwinkel N, Ciuffi A. (2017) Dynamics of Proteo-Transcriptomic Response to HIV-1 Infection.

Examples

# Load the toy time series data provided with the TMixClust package
data(toy_data_df)

# Cluster the toy data with default parameters
TMixClust_obj = TMixClust(toy_data_df)

cbg-ethz/TMixClust documentation built on May 30, 2019, 8:28 a.m.