seedset-class {RevEcoR} | R Documentation |
seedset-class
Description
Object representing the seed sets of a given metabolic network
Slots
GsMN,
a igraph network
seeds,
a character list represents seeds of a given metabolic network which is composed of the KEGG compound index.
method
getGsMN,
signature(object = "seedset")
: get the genome scale metabolic network whose seed set is caculatedlen,
signature(object = "seedset")
: return the number of source SCCseedSize,
signature(object = "seedset")
: returns the sizes of each source SCCsnonseed,
signature(object = "seedset")
: the non seeds of the GsMNshow,
signature(object = "seedset")
: show the short summary of a seedset classconfidencescore,
signature(object = "seedset")
: confidence score of the seed set
See Also
getSeedSets
,getGsMN
,len
,
nonseed
,seedSize
,confidencescore
Examples
## Not run:
#' ## generate a metabolic network in igraph class and a seed set of this graph
annodir <- system.file("extdata","koanno.tab",package = "RevEcoR")
metabolic.data <- read.delim2(file=annodir,stringsAsFactors=FALSE)
g <- reconstructGsMN(metabolic.data)
seeds <- getSeedSets(g)@seeds
seed.set <- new("seedset",GsMN = g, seeds = seeds)
## End(Not run)
[Package RevEcoR version 0.99.3 Index]