In the process of conducting joint-pathway analysis by MetaboAnalystR, there is an error raised when using the command mSet<-PerformGeneMapping(mSet, geneList, “hsa”, “symbol”); as ’ ‘Error: no such table: entrez’ '. Based my debug process, it seems to origin from the ‘doGeneIDMapping’ Function.
Here are my codes and session:
I tried for hours to solve the problem. These errors occur due to the lack of the hsa_genes.sqlite file in the working directory, which can be downloaded here:
doGeneIDMapping ← function(q.vec, org, type){
print(org)
sqlite.path ← paste0(url.pre, org, “_genes.sqlite”);
if(!file.exists(sqlite.path)){
#“https://www.xialab.ca/resources/sqlite/hsa_genes.sqlite”
sqlite_url ← paste0(“https://www.xialab.ca/resources/sqlite/”,
org, “_genes.sqlite”);
sqlite.path ← paste0(getwd(), “/”,org, “_genes.sqlite”)
download.file(sqlite_url,destfile = sqlite.path, method = “curl”)
}
