Question: Modifying a Pathview function which needs an internet connection so that it can work without an internet connection.
0
gravatar for omarrafiqued
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) 
{
  keggpathid2extid.df <- kegg_link(species, "pathway")
  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
ADD COMMENTlink modified 3 months ago • written 3 months ago by omarrafiqued50
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 151 users visited in the last hour