Map Gene names/IDs on Pathway with KEGG
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Entering edit mode
5.6 years ago
Shelle ▴ 30

I want to map the list of gene IDs that i have to pathway and see if there is a pathway between the genes. I decided to go with KEGG using the code below to see what can be the name of nodes given the pathway id but for some reason in one line it gives me error so i am not able to run the code in the documentation website. https://www.bioconductor.org/packages/devel/bioc/vignettes/KEGGgraph/inst/doc/KEGGgraph.pdf

Does anyone know how this problem can be solved?

> library(KEGG.db)
> tmp <- tempfile()
> pName <- "Metabolic pathways"
> pId <- mget(pName, KEGGPATHNAME2ID)[[1]]
> retrieveKGML(pId, organism="cel", destfile=tmp, method="wget", quiet=TRUE)
> mapkKGML <- system.file("extdata/hsa01100.xml", package="KEGGgraph")

# Error was in the line above: 
Error in if (fileSize < 100L) msg <- paste(msg, "[WARNING] File size (",  :
  missing value where TRUE/FALSE needed

> mapkG <- parseKGML2Graph(mapkKGML,expandGenes=TRUE)
> mapkNodes <- nodes(mapkG)
> nodes(mapkG)[1:3]

The only change here comparing to the documentation is the pathway identifier i have also tried their exact example and same issue.

Pathway KEGG gene • 2.1k views
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Entering edit mode
5.6 years ago
h.mon 35k

A quick careful reading of the KEGGgraph manual will tell you the cause of the failure, which can be confirmed with:

list.files( system.file( "extdata/", package = "KEGGgraph" ) )
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