Modifying a Pathview function which needs an internet connection so that it can work without an internet connection.
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omarrafiqued ▴ 50
Last seen 4 months ago

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 ''...

function (species) 
  keggpathid2extid.df <- kegg_link(species, "pathway")
  if (is.null(keggpathid2extid.df)) 
    stop("'species' should be one of organisms listed in ''...")
  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 Gene Mapping KEGG • 1.0k views

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