R/kegg_summary.R

In w-korani/keggseq: KEGG analysis and visualizing of differentially expressed genes

#'name kegg_summary
kegg_summary <- function(dataset)
{
    requireNamespace('qvalue')
    Results = cbind(dataset,
    qvalue=qvalue::qvalue(dataset$pvalue)$qvalue)
    Link1 = "http://rest.kegg.jp/list/pathway"
    Table1 = readLines(Link1)
    Table2 = t(data.frame(strsplit(Table1,'\t')))
    Table3 = cbind(map_numbers = as.character(Table2[,1]),
    pathway_description = as.character(Table2[,2]))
    Table4 = gsub('path:map','',Table3)
    Table5 = data.frame(Table4)
    Table6 = merge(Table5,Results,by="map_numbers")
    Table7 = Table6[,c(1,2,3,4,5,6,8)]
    return(Table7)
}