infere.con2ec: Infer connections to EC

In b2slab/FELLA: Interpretation and enrichment for metabolomics data

Description

Function infere.con2ec infers network connections to KEGG EC families by passing through genes. This assumes that the category being mapped to enzymes is above them.

Usage

infere.con2ec(ids, ent, ent2gene, gene2enzyme)

Arguments

ids	Character vector of identifiers to map. For example, all the KEGG pathways
ent	Character, entity that we are mapping (one of "pathway" and one of "module")
ent2gene	Named character vector, names are the entity ent and values are genes
gene2enyzme	Named character vector, names are genes and values are EC enzyme families category Character, one of:

Value

Two-column data frame. Column "from" contains the KEGG enzyme families whereas "to" contains the entity ent.

Examples

ids <- "hsa00010"
ent <- "pathway"
ent2gene <- c("hsa00010" = "hsa:10", "hsa00010" = "hsa:120")
gene2enzyme <- c("hsa:10" = "1.1.1.1", "hsa:120" = "1.2.3.4")
FELLA:::infere.con2ec(ids, ent, ent2gene, gene2enzyme)

b2slab/FELLA documentation built on March 3, 2021, 2:22 p.m.