getSeedSets {RevEcoR} | R Documentation |
Identify seed compounds of each organism
Description
Detect a given metabolic network and idendity the seed compounds of each organism
Usage
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. |
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.
Value
a two-length list which consists of network and the seed set compounds of the given organism-specific metabolic network, ....
See Also
Examples
## Not run:
## get metabolic annotated data of a specific species
metabolic.data <- getOrgMetabolicData("buc")
## metabolic network reconstruction
net <- reconstructGsMN(metabolic.data)
## End(Not run)
[Package RevEcoR version 0.99.3 Index]