Question: Modifying a Pathview function which needs an internet connection so that it can work without an internet connection.
0
3 months ago by
omarrafiqued50
omarrafiqued50 wrote:

For the following code, when there is no internet connection, I get the error "Error in download.KEGG.Path(species) : 'species' should be one of organisms listed in 'http://www.genome.jp/kegg/catalog/org_list.html'...

function (species)
{
if (is.null(keggpathid2extid.df))
stop("'species' should be one of organisms listed in 'http://www.genome.jp/kegg/catalog/org_list.html'...")
keggpathid2extid.df[, 1] %<>% gsub("[^:]+:", "", .)
keggpathid2extid.df[, 2] %<>% gsub("[^:]+:", "", .)
keggpathid2name.df <- kegg_list("pathway")
keggpathid2name.df[, 1] %<>% gsub("path:map", species, .)
keggpathid2extid.df <- keggpathid2extid.df[keggpathid2extid.df[,
1] %in% keggpathid2name.df[, 1], ]
return(list(KEGGPATHID2EXTID = keggpathid2extid.df, KEGGPATHID2NAME = keggpathid2name.df))
}


Is there any way I could use the above function when I don't have internet connection.

Or is there any other package which will give me similar results without using internet.

pathview kegg gene mapping • 86 views