Identify seed compounds of each organism

Detect a given metabolic network and idendity the seed compounds of each organism

getSeedSets(g, threshold = 0)

Arguments

g,

an igraph object which represents a given organism-specific metaboliic network

threshold,

numeric constant ranges from 0 to 1, default is 0.

Value

a two-length list which consists of network and the seed set compounds of the given organism-specific metabolic network, ....

Details

All the compound in the same source SCC all equally to be included in the seed set, each of these compounds was assigned a confidence level, C=1/(size of souce SCC), denoting the compounds probability of being a seed. This threshold was used to determin whether a compound should be a seed.

See also

KosarajuSCC,seedset-class

Examples

## Not run: ------------------------------------
# ## get metabolic annotated data of a specific species
# metabolic.data <- getOrgMetabolicData("buc")
# ## metabolic network reconstruction
# net <- reconstructGsMN(metabolic.data)
## ---------------------------------------------