RevNet.ZeroSlopesMethod: Reverse engineering of networks: zero slopes method

In MetStaT: Statistical metabolomics tools

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.

Author(s)

Diana Hendrickx and Tim Dorscheidt

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

Examples

data(RevNetZeroSlopes)
RevNet.ZeroSlopesMethod(RevNetZeroSlopes, 0.001, 0.00005)

MetStaT documentation built on May 2, 2019, 1:45 p.m.