TDCor algorithm for gene regulatory network inference

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Description

TDCor (Time-Delay Correlation) is an algorithm designed to infer the topology of a gene regulatory network (GRN) from time-series transcriptomic data. The algorithm is described in details in Lavenus et al., Plant Cell, 2015. It was initially developped to infer the topology of the GRN controlling lateral root formation in Arabidopsis thaliana. The time-series transcriptomic dataset analysed in this study is included in the package.

Details

Package: TDCor
Type: Package
Version: 1.2
Date: 2015-10-05
License: GNU General Public License Version 2

The reconstruction of a gene network using the TDCor package involves six steps.

  1. Load the averaged non-log2 time series transcriptomic data into the R workspace.

  2. Define the vector times containing the times (in hours) at which the samples were collected.

  3. Define the vector containing the gene codes of the genes you want to reconstruct the network with (e.g. see l_genes), as well as the associated gene names (e.g. see l_names) and the associated prior (e.g. see l_prior).

  4. Build or update the TPI database using the CalculateTPI or UpdateTPI functions.

  5. Build or update the DPI database using the CalculateDPI or UpdateDPI functions.

  6. Reconstruct the network using the TDCOR main function.

See examples below.

Besides the functions of the TDCor algorithm, the package also contains the lateral root transcriptomic dataset (LR_dataset), the times vector to use with this dataset (times), the vector of AGI gene codes used to reconstruct the network shown in the original paper (l_genes), the vector of the gene names (l_names) and the prior (l_prior). The associated TPI and DPI databases (TPI10 and DPI15) which were used to build the network shown in the original paper are not included. Hence to reconstruct the lateral root network, these first need to be generated. A database of about 1800 Arabidopsis transcription factors is also included (TF).

Three side functions, estimate.delay, shortest.path and draw.profile are also available to the user. These can be used to visualize the transcriptomic data, optimize some of the TDCOR parameters, and analyze the networks.

Author(s)

Author: Julien Lavenus jl.tdcor@gmail.com
Maintainer: Mikael Lucas mikael.lucas@ird.fr

References

Lavenus et al. (2015), Inference of the Arabidopsis lateral root gene regulatory network suggests a bifurcation mechanism that defines primordia flanking and central zones. The Plant Cell, in press.

See Also

See also CalculateDPI, CalculateTPI, UpdateDPI, UpdateTPI, TDCOR, estimate.delay.

Examples

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

# Load the vectors of genes 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)

# Generate the TPI database (this may take several hours) 

TPI10=CalculateTPI(dataset=LR_dataset,l_genes=l_genes,l_prior=l_prior, 
times=times,time_step=1,N=10000,ks_int=c(0.5,3),kd_int=c(0.5,3), 
delta_int=c(0.5,3),noise=0.1,delay=3)

# Generate the DPI database (this may take several hours) 

DPI15=CalculateDPI(dataset=LR_dataset,l_genes=l_genes,l_prior=l_prior, 
times=times,time_step=1,N=10000,ks_int=c(0.5,3),kd_int=c(0.5,3), 
delta_int=c(0.5,3), noise=0.15, delay=3)

# Check/update if necessary the databases

TPI10=UpdateTPI(TPI10,LR_dataset,l_genes,l_prior)
DPI15=UpdateDPI(DPI15,LR_dataset,l_genes,l_prior)

# Choose your parameters 

ptime_step=1			
ptol=0.13			
pdelayspan=12			
pthr_cor=c(0.65,0.8)	
pdelaymax=c(2.5,3.5)		
pdelaymin=0			
pdelay=3			
pthrpTPI=c(0.55,0.8)		
pthrpDPI=c(0.65,0.8)		
pthr_overlap=c(0.4,0.6)		
pthr_ind1=0.65			
pthr_ind2=3.5			
pn0=1000			
pn1=10				
pregmax=5					
pthr_isr=c(4,6)			
pTPI=TPI10			
pDPI=DPI15			
pMinTarNumber=5			
pMinProp=0.6			
poutfile_name="TDCor_output.txt"	


# Reconstruct the network

tdcor_out= TDCOR(dataset=LR_dataset, l_genes=l_genes,l_names=l_names,n0=pn0,n1=pn1,
l_prior=l_prior, thr_ind1=pthr_ind1,thr_ind2=pthr_ind2,regmax=pregmax,thr_cor=pthr_cor,
delayspan=pdelayspan,delaymax=pdelaymax,delaymin=pdelaymin,delay=pdelay,thrpTPI=pthrpTPI,
thrpDPI=pthrpDPI,TPI=pTPI,DPI=pDPI,thr_isr=pthr_isr,time_step=ptime_step,thr_overlap=pthr_overlap,
tol=ptol,MinProp=pMinProp,MinTarNumber=pMinTarNumber,outfile_name=poutfile_name)


## End(Not run)