generate_TMixClust_report: Generates a series of files containing a summary of the...

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

Description

generate_TMixClust_report

Usage

generate_TMixClust_report(TMixClust_object, report_folder = paste(getwd(),
  "/TMixClust_report/", sep = ""), data_color = "#fd8d3c", x_label = "time",
  y_label = "value")

Arguments

TMixClust_object	list object created by the TMixClust function (see function TMixClust)
report_folder	full path of the folder where the report files will be saved. Default is TMixClust_report/ folder in current working directory.
data_color	color of the time series to be used when generating the cluster plots. Default is orange.
x_label	label of the x axis for the cluster plots. Default is "time"
y_label	label of the y axis for the cluster plots. Default is "value"

Value

Produces a series of files containing information about the clustering results and saves them in the provided folder location. The folder contains the following:

• log-lihelihood.txt - file with the log likelihood values at each iteration on separate lines

• log-likelihood.pdf - plot of log-likelihood at each iteration

• posterior.txt - file with the posterior probabilities of all the time-series for each cluster

• estimated_curves/ - folder containing a number of files equal to the number of clusters; each file has 4 lines consisting of curve values and their confidence intervals (first 3 lines) for a discrete time grid (last line).

• clusters/ - folder containing a plot with the time series in each cluster, a silhouette plot of the clustering configuration, as well as, for each cluster, a file containing the names of the time series in the respective cluster and a file containing the names and time series values for the time series in each cluster.

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

## Not run: 
# 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)

# Generate a TMixClust report in the current working directory
generate_TMixClust_report(TMixClust_obj)

## End(Not run)

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