From: vandersm <vandersm@mail.uc.edu>
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGlincs@126853 bc3139a8-67e5-0310-9ffc-ced21a209358
Shana White authored on 21/02/2017 18:16:40
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+#' Import disease/drug tables from KEGG |
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+#' @description Get data tables for disease/drug information associated with |
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+#' selected pathway |
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+#' @param pathwayid A KEGG pathway ID of the form "hsa12345" |
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+#' (only human pathways currently) |
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+#' @return A data.frame object with either disease or drug information |
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+#' @export |
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+#' @examples |
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+#' RA_drug_table <- get_drug_table("hsa05323")
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+ |
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+get_drug_table <- function(pathwayid){
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+ |
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+ url <- paste0("http://www.kegg.jp/kegg-bin/pathway_dd_list?map=",
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+ pathwayid) |
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+ dd_table <- data.frame( |
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+ XML::readHTMLTable(url, header = T, which = 4, as.data.frame = FALSE), |
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+ stringsAsFactors = FALSE) |
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+ if (nrow(dd_table) > 0){
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+ d_table <- subset(dd_table, substring(dd_table$Disease.drug, 1, 1) == "D") |
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+ if(nrow(d_table) == 0){
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+ warning("No associated drug targets in selected pathway")
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+ return() |
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+ } |
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+ return(d_table) |
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+ } |
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+ else {
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+ warning("No drugs or diseases associated with selected pathway")
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+ return() |
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+ } |
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+} |
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+#' @rdname get_drug_table |
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+get_disease_table <- function(pathwayid){
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+ |
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+ url <- paste0("http://www.kegg.jp/kegg-bin/pathway_dd_list?map=",
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+ pathwayid) |
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+ dd_table <- data.frame( |
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+ XML::readHTMLTable(url, header = T, which = 4, as.data.frame = FALSE), |
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+ stringsAsFactors = FALSE) |
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+ if (nrow(dd_table) > 0){
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+ d_table <- subset(dd_table, substring(dd_table$Disease.drug, 1, 1) == "H") |
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+ if(nrow(d_table) == 0){
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+ warning("No diseases associated with selected pathway")
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+ return() |
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+ } |
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+ return(d_table) |
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+ } |
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+ else {
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+ warning("No drugs or diseases associated with selected pathway")
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+ return() |
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+ } |
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+} |
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+ |
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+#' @examples |
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+#' RA_disease_table <- get_disease_table("hsa05323")
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+% Generated by roxygen2: do not edit by hand |
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+% Please edit documentation in R/get_dd_tables.R |
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+\name{get_drug_table}
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+\alias{get_disease_table}
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+\alias{get_drug_table}
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+\title{Import disease/drug tables from KEGG}
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+\usage{
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+get_drug_table(pathwayid) |
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+ |
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+get_disease_table(pathwayid) |
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+} |
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+\arguments{
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+\item{pathwayid}{A KEGG pathway ID of the form "hsa12345"
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+(only human pathways currently)} |
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+} |
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+\value{
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+A data.frame object with either disease or drug information |
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+} |
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+\description{
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+Get data tables for disease/drug information associated with |
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+selected pathway |
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+} |
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+\examples{
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+RA_drug_table <- get_drug_table("hsa05323")
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+} |
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+ |