caculateCooperationIndex: Caculating the metabolic competition and complementarity index
Description
Caculating the metabolic competition complementarity index among all metabolic
networks
Usage
caculateCooperationIndex(g, ..., threshold = 0)
Arguments
g,
igraph that represents a metabolic network, see reconstructGsMN
...,
a list of metabolic networks or a network append to g
threshold
threshold, the cutoff of confidence score to be serve as a
seed set, default is 0.2
Value
a cooperation index matrix whose nrow and ncol is equal to the number
of species to be compared, for more see details.
Details
Metabolic competition index is defined as the fraction of compounds
in a species seed set of metabolic network that are alse included in its
partner; However, metabolic complementarity index is the fraction of
compounds in one species seed set of metabolic network appearing in the
metabolic network but not in the seed set of its partner; The biosynthetic
support score represents the extent to which the metabolic requirements of a
potential parasitic organism can be supported by the biosynthetic capacity of
a potential host. It is measured by calculating the fraction of the source
components of a, in which at least one of the compounds can be found in the
network of b. However, seed compounds are associated with a confidence score
(1/size of SCC), so this fraction is calculated as a mormalized weighted sum.
The ith row and jth col elements of the returnd matrix represents the
metabolic competition index or complementarity index of the ith network on the
jth metabolic network.