expand_KEGG_mappings: Get detailed KEGG mapping information for each map entity

In KEGGlincs: Visualize all edges within a KEGG pathway and overlay LINCS data

Description

Extract mapping information from KGML object and normalize mappings based on multi-valued name attribute

Usage

expand_KEGG_mappings(KGML_file, convert_KEGG_IDs = TRUE)

Arguments

KGML_file

An object of formal class KEGGPathway

convert_KEGG_IDs

A logical indicator; if set to FALSE will run faster however genes and compounds will remain labeled via KEGG codes (compounds) or accession numbers (genes). This option must be taken into account if data is being added. For example, the genes in 'KO_data' are identified by symbols, thus it is neccessary to retain the default option to convert IDs to symbols when planning to add edge data of this type.

Value

A dataframe object with unique entry information for all [node] objects documented in the KEGG pathway. Note that if mutiple objects (i.e. genes or compounds) have the same entryID, this indicates that they share the same node [location] in the pathway.

Examples

p53_KGML <- get_KGML("hsa04115")
p53_KEGG_mappings <-  expand_KEGG_mappings(p53_KGML, FALSE)

KEGGlincs documentation built on Nov. 8, 2020, 5:47 p.m.