RevNet.ZeroSlopesMethod:
Reverse engineering of networks: zero slopes method
Description
Network connections are estimated by analyzing concentration profiles, whereby non-zero slopes possibly indicate a network connection.
Details of algorithm and the theory behind the algorithm can be found in the references section. This method needs very high frequency sampling data of single variable perturbations.
Usage
RevNet.ZeroSlopesMethod(X, deltat, threshold)
Arguments
X
multi-dimensional sampling matrix: time x variables x experiments
deltat
single value indicating the time difference between sampling moments
threshold
threshold for determining whether an edge is assumed or not; affects network-sparsity.
Value
A connectivity matrix is returned.
References
Reverse engineering of metabolic networks, a critical assessment. Diana M. Hendrickx, Margriet M. W. B. Hendriks, Paul H. C. Eilers, Age K. Smilde and Huub C. J. Hoefsloot. Mol. BioSyst, Volume 7:2 (2011) pages 511-520