Takes a vector of KEGG pathway ids and retrieves graph representation (KGML), and subsequently translates the KEGG IDs for each ndoe into gene ids (SYMBOL or ENSEMBL).

TranslateKEGGPathway(keggpathid, organism = "mmu", geneDB = NULL,
  identifier = "SYMBOL", keepKGML = FALSE)

Arguments

keggpathid

character vector of KEGG pathway ids (e.g. "mmu00010")

organism

organism of interest ("mmu" or "hsa") for KGML retrieval

geneDB

data.frame consisting of at minimum, your chosen identifier (SYMBOL by default); this could be the first two columns of output from TranslateENSEMBL, which translates a DESeq2 dds object into SYMBOL and ENSEMBL

identifier

the chosen identifier to use; currently only supports SYMBOL and ENSEMBL usage [default: SYMBOL]

keepKGML

choose whether to keep the .kgml file that is retrieved (default: FALSE)

Value

graphNEL object; for multiple pathways, returns a list of graphNEL objects

Examples

res <- TranslateENSEMBL(results(dds))
path <- "mmu00010"
TranslateKEGGPathway(path, geneDB = res$SYMBOL, keepKGML = TRUE)