UpdateDPI: Update or check the DPI database

In TDCor: Gene Network Inference from Time-Series Transcriptomic Data

Description

UpdateDPI analyzes the DPI database and add new entries into it if it does not contain all the necessary data for reconstructing the network with the genes listed in the vector l_genes.

Usage

UpdateDPI(DPI,dataset,l_genes, l_prior)

Arguments

DPI	The DPI database to update or check before reconstructing the network.
dataset	Numerical matrix storing the transcriptomic data. The rows of this matrix must be named by gene codes (like AGI gene codes for Arabidopsis data).
l_genes	A character vector containing the gene codes of the genes we want to reconstruct the network with.
l_prior	A numerical vector containing the prior information on the genes included in the network recontruction. By defining the l_prior vector, the user defines which genes should be regarded as positive regulators, which others as negative regulators and which can only be targets. The prior code is defined as follow: -1 for negative regulator; 0 for non-regulator (target only); 1 for positive regulator; 2 for both positive and negative regulator. The i-th element of the vector is the prior to associate to the i-th gene in l_genes.

Value

UpdateDPI returns an updated DPI database containing data for at least all the genes in l_genes whose associated prior is not null.

Author(s)

Julien Lavenus [e-mail]

See Also

See also CalculateDPI.

Examples

## Not run: 
# Load the Lateral root transcriptomic dataset
data(LR_dataset)

# Load the vector of gene codes, gene names and prior
data(l_genes)
data(l_names)
data(l_prior)

# Load the vector of time points for the LR_dataset
data(times)

# Build a very small DPI database (3 genes)
DPI_example=CalculateDPI(dataset=LR_dataset,l_genes=l_genes[4:6],l_prior=l_prior[4:6],
times=times,time_step=1,N=5000,ks_int=c(0.5,3),kd_int=c(0.5,3),delta_int=c(0.5,3),
noise=0.15,delay=3)

# Add one gene in the database
DPI_example=UpdateDPI(DPI_example,dataset=LR_dataset,l_genes[4:7],l_prior[4:7])

## End(Not run)

TDCor documentation built on May 2, 2019, 3:41 p.m.