specmine (version 3.1.6)

get_paths_with_cpds_org: Get only the paths of the organism that contain one or more of the given compounds.

Description

Gives only the metabolic paths of the mentioned organism that contain one or more of the given compounds.

Usage

get_paths_with_cpds_org(organism_code, compounds, full.result=TRUE)

Arguments

organism_code

Organism code. The correct code for an organism can be consulted using function get_OrganismsCodes.

compounds

Named vector with kegg codes of compounds and respective names. This vector can be obtained by using the function get_cpd_names or the function convert_hmdb_to_kegg.

full.result

If the full result is to be given. Defaults to TRUE.

Value

Data frame.

If full result is chosen, the data frame contains information on the pathways of the organism that contains one or more of the given compounds and, for each pathway, the kegg codes (and their names) of the compounds given that are present in that path. The ratio between the number of compounds given compounds present in each pathway and the total number of compounds in each pathway is also given, full result or not.

If full result is not wanted, only the pathways will be given.

Examples

# NOT RUN {
#Get human metabolic paths that have one or more of the three following compounds
keggs=get_cpd_names(c("cpd:C00033", "cpd:C00147", "gl:G13099"))
paths_org_cpds=get_paths_with_cpds_org("hsa", keggs)
paths_org_cpds
# }