traceGeneProfiles: Function to plot the gene expression profiles

In ARTIVA: Time-Varying DBN Inference with the ARTIVA (Auto Regressive TIme VArying) Model

Description

This function is used for plotting the target and parent gene expression profiles.

Usage

traceGeneProfiles(targetData, parentData,  dataDescription=NULL,
targetColor = "grey", parentColor = "blue", onepage=TRUE)

Arguments

targetData	A matrix (or a vector if only one target gene) with the temporal gene expression measurements for the target genes (i.e. the genes whose regulation factors are looked for). Target genes are shown in row and expression values in column.
parentData	A matrix (or a vector if only 1 parent gene) with the temporal gene expression measurements for the proposed parent genes (i.e. potential regulation factors). Parent genes are shown in row and expression values in column.
dataDescription	(Required only when the gene expression measurements contain repeated values for the same time points). A vector indicating the ordering of the time measurements in the data. For example dataDescription=rep(1:n, each=2), if there are two measurements for each time point AND the repetitions for each time point are next to each other. Note that temporal gene expression measurements have to be organized identically in arguments targetData and parentData (optional, default: dataDescription=NULL).
targetColor	Color for plotting the target genes expression profiles (optional, default targetColor= "grey")
parentColor	Color for plotting the parent genes expression profiles (optional, default parentColor= "blue")
onepage	Boolean, if TRUE, all output pictures are plotted on one page only (optional, default: onepage=TRUE.

Value

NULL

Author(s)

S. Lebre and G. Lelandais.

References

Statistical inference of the time-varying structure of gene-regulation networks S. Lebre, J. Becq, F. Devaux, M. P. H. Stumpf, G. Lelandais, BMC Systems Biology, 4:130, 2010.

See Also

ARTIVAsubnet, ARTIVAnet

Examples

# Load the R package ARTIVA
library(ARTIVA)

# Load the dataset with simulated gene expression profiles
data(simulatedProfiles)

# Name of the target gene to be analyzed with ARTIVA 
targetGene = 1

# Names of the parent genes (typically transcription factors) 
parentGenes = c("TF1", "TF2", "TF3", "TF4", "TF5")

# Plot of the gene expression profiles for target gene and parent genes
traceGeneProfiles(targetData= simulatedProfiles[targetGene,], 
		  parentData= simulatedProfiles[parentGenes,])

ARTIVA documentation built on May 1, 2019, 6:31 p.m.