seedset-class: 'seedset-class'

In RevEcoR: Reverse Ecology Analysis on Microbiome

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 caculated

• len, signature(object = "seedset"): return the number of source SCC

• seedSize, signature(object = "seedset"): returns the sizes of each source SCCs

• nonseed, signature(object = "seedset"): the non seeds of the GsMN

• show, signature(object = "seedset"): show the short summary of a seedset class

• confidencescore, 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)

RevEcoR documentation built on May 2, 2019, 1:06 p.m.