Hi there! I'm new in this community as I'm new with R and happy to deal with it. The aim of my project is to define connections between genes and their pathways, to do this I'm trying to retrieve the pathways from KEGG. Following the KEGGgraph tutorial I figured out with an ERROR that don't understand. Someone of you could help me please?
library(KEGGgraph)
library(KEGGREST)
library(RBGL)
library(org.Hs.eg.db)
library(devtools)HIF1A_pathways <- c("hsa04066.xml", "hsa04137.xml", "hsa04140.xml",
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"hsa04659.xml", "hsa04919.xml", "hsa05167.xml",
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"hsa05200.xml", "hsa05205.xml", "hsa05208.xml",
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"hsa05211.xml", "hsa05230.xml", "hsa05231.xml",
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"hsa05235.xml")
HIF1A_pfiles <- system.file(paste("/extdata/", HIF1A_pathways, sep=""), package="KEGGgraph")
mapHIF1A<- parseKGML2Graph("hsa04066.xml",genesOnly = TRUE, expandGenes =TRUE)
Error in if (fileSize < 100L) msg <- paste(msg, "[WARNING] File size (", : **
** missing value where TRUE/FALSE needed