kegg_reconstruction {metabolism} R Documentation

do kegg pathway reconstruction by given protein annotation data

Description

Usage

kegg_reconstruction(reference, reactions, annotations,
    min.cov = 0.3,
    prefix = NULL);

Arguments

reference

the kegg reference maps

reactions

a list of the kegg reaction data models

annotations

the ProteinAnnotation data stream with kegg ontology('ko' attribute) id.

min.cov

coverage cutoff of the ratio of annotation protein hit against the all proteins on the pathway map. [as double]

env

[as Environment]

Details

Authors

kegg_kit

Value

A set of the kegg pathway object that contains with the KEGG id mapping(protein id mapping and assigned compound id list)

clr value class

Examples

[Package metabolism version 1.0.0.0 Index]