infere.con2ec {FELLA}R Documentation

Infer connections to EC

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)
[Package FELLA version 1.2.0 Index]