constructSSN: construct the state specific network

In mmnet: A metagenomic pipeline for systems biology

Description

Given a set of KOs of a sample with a specific state and the reference metabolic network, this function creates and returns sub-network with only the supplied nodes (KOs) and any edges between them.

Usage

constructSSN(abundance)

Arguments

abundance

abundance of KOs of a given specific state, may a numeric vector which can be obtained with estimateAbundance a given Biological Observation Matrix (BIOM) format, the ncol of BIOM file represents number of samples. The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. More details on BIOM file can be found in http://biom-format.org/ R package biom. There is also a example BIOM file in directory "inst/extdata" of mmnet. It could be obtained with estimateAbundance. Moreover, while samples has been annotated with other tools (e.g. blast to KEGG locally), users could create their own BIOM file represents enzymatic genes abundance.

Details

Reference metabolic network has been saved in the RefDbcache. There are varies sets of KOs and its abundance between metagenomic samples. With this function, users can create a specified sub-network of the reference network for each sample.

Value

new graph object will be return, and the abundance is added as a vertex meta-attributes. The number of graph is equal to the samples.

See Also

RefDbcache, estimateAbundance

Examples

# load reference metabolic network 
data(RefDbcache)

data(anno)
abund <- estimateAbundance(anno[[1]])
subnet  <- constructSSN(abund)

mmnet documentation built on May 31, 2017, 3:25 p.m.