From: vandersm <vandersm@mail.uc.edu>
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGlincs@127001 bc3139a8-67e5-0310-9ffc-ced21a209358
Shana White authored on 27/02/2017 17:26:16
| 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,62 @@ |
| 1 |
+#' Add edges from disease/drug tables |
|
| 2 |
+#' @description Expand edge mappings to include drugs/drug targets |
|
| 3 |
+#' for selected pathway |
|
| 4 |
+#' @param edges A data.frame object obtained by using the function `expand_kegg_edges` |
|
| 5 |
+#' @param KEGG_mappings A data.frame object obtained by using the function `expand_kegg_mappings` |
|
| 6 |
+#' @param kegg_drug_table A data.frame object obtained by using the function `get_drug_table` |
|
| 7 |
+#' @return A data.frame object similar to the expanded edges data frame but with additional |
|
| 8 |
+#' edges representing known drugs/drug targets |
|
| 9 |
+#' @export |
|
| 10 |
+#' @examples |
|
| 11 |
+ |
|
| 12 |
+#' end_res_KGML <- get_KGML("hsa01522")
|
|
| 13 |
+#' end_res_KEGG_mappings <- expand_KEGG_mappings(end_res_KGML) |
|
| 14 |
+#' end_res_edges <- expand_KEGG_edges(end_res_KGML, end_res_KEGG_mappings) |
|
| 15 |
+ |
|
| 16 |
+#' end_res_drugs <- get_drug_table("hsa01522")
|
|
| 17 |
+ |
|
| 18 |
+#' edges_plus_kdrug <- add_kegg_drugs(end_res_edges, end_res_KEGG_mappings, end_res_drugs) |
|
| 19 |
+ |
|
| 20 |
+add_kegg_drugs <- function(edges, KEGG_mappings, kegg_drug_table){
|
|
| 21 |
+ |
|
| 22 |
+ edges$u_ID <- paste0(edges$entry1accession,":", edges$entry2accession) |
|
| 23 |
+ kegg_drug_table$u_ID <- paste0(kegg_drug_table$drug_KEGG_ID,":", kegg_drug_table$gene_id) |
|
| 24 |
+ |
|
| 25 |
+ drugs_to_add <- subset(kegg_drug_table, !kegg_drug_table$u_ID %in% edges$u_ID) |
|
| 26 |
+ edges_to_add <- data.frame( |
|
| 27 |
+ "edgeID" = seq(from = (1 + max(edges$edgeID)), to = (nrow(drugs_to_add) + max(edges$edgeID))), |
|
| 28 |
+ "entry1accession" = drugs_to_add$drug_KEGG_ID, |
|
| 29 |
+ "entry2accession" = drugs_to_add$gene_id, |
|
| 30 |
+ "entry1" = NA, |
|
| 31 |
+ "entry2" = NA, |
|
| 32 |
+ "type" = "PCrel", |
|
| 33 |
+ "subtype1" = "from_kegg_drug", |
|
| 34 |
+ "value" = "--", |
|
| 35 |
+ "subtype2" = NA, |
|
| 36 |
+ "value2" = NA, |
|
| 37 |
+ "specific_subtype" = "from_kegg_drug", |
|
| 38 |
+ "is_direct" = 1, |
|
| 39 |
+ "entry1type" = "compound", |
|
| 40 |
+ "entry2type" = "gene", |
|
| 41 |
+ "entry1symbol" = drugs_to_add$drug_name, |
|
| 42 |
+ "entry2symbol" = drugs_to_add$gene_symbol, |
|
| 43 |
+ "u_ID" = drugs_to_add$u_ID, |
|
| 44 |
+ stringsAsFactors = FALSE |
|
| 45 |
+ ) |
|
| 46 |
+ for (i in 1:nrow(edges_to_add)){
|
|
| 47 |
+ edges_to_add$entry2[i] <- KEGG_mappings$entryID[KEGG_mappings$entryACCESSION == |
|
| 48 |
+ edges_to_add$entry2accession[i]][1] |
|
| 49 |
+ if (edges_to_add$entry1accession[i] %in% KEGG_mappings$entryACCESSION){
|
|
| 50 |
+ edges_to_add$entry1[i] <- KEGG_mappings$entryID[KEGG_mappings$entryACCESSION == |
|
| 51 |
+ edges_to_add$entry1accession[i]][1] |
|
| 52 |
+ } |
|
| 53 |
+ } |
|
| 54 |
+ # Decide whether or not to map to all nodes of gene on map |
|
| 55 |
+ # for (i in 1:nrow(edges_to_add)){
|
|
| 56 |
+ # edges_to_add$entry2[i] <- list(KEGG_mappings$entryID[KEGG_mappings$entryACCESSION == edges_to_add$entry2accession[i]]) |
|
| 57 |
+ # } |
|
| 58 |
+ all_edges <- rbind(edges[, -c(17)], edges_to_add[, -c(17)]) |
|
| 59 |
+ |
|
| 60 |
+} |
|
| 61 |
+ |
|
| 62 |
+#load("/opt/raid10/genomics/shana/KEGG_drug_targets/via_cts_convert/compound_cgs_KEGG_filtered.rda")
|
| 0 | 63 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,31 @@ |
| 1 |
+% Generated by roxygen2: do not edit by hand |
|
| 2 |
+% Please edit documentation in R/add_kegg_drugs.R |
|
| 3 |
+\name{add_kegg_drugs}
|
|
| 4 |
+\alias{add_kegg_drugs}
|
|
| 5 |
+\title{Add edges from disease/drug tables}
|
|
| 6 |
+\usage{
|
|
| 7 |
+add_kegg_drugs(edges, KEGG_mappings, kegg_drug_table) |
|
| 8 |
+} |
|
| 9 |
+\arguments{
|
|
| 10 |
+\item{edges}{A data.frame object obtained by using the function `expand_kegg_edges`}
|
|
| 11 |
+ |
|
| 12 |
+\item{KEGG_mappings}{A data.frame object obtained by using the function `expand_kegg_mappings`}
|
|
| 13 |
+ |
|
| 14 |
+\item{kegg_drug_table}{A data.frame object obtained by using the function `get_drug_table`}
|
|
| 15 |
+} |
|
| 16 |
+\value{
|
|
| 17 |
+A data.frame object similar to the expanded edges data frame but with additional |
|
| 18 |
+edges representing known drugs/drug targets |
|
| 19 |
+} |
|
| 20 |
+\description{
|
|
| 21 |
+Expand edge mappings to include drugs/drug targets |
|
| 22 |
+for selected pathway |
|
| 23 |
+} |
|
| 24 |
+\examples{
|
|
| 25 |
+end_res_KGML <- get_KGML("hsa01522")
|
|
| 26 |
+end_res_KEGG_mappings <- expand_KEGG_mappings(end_res_KGML) |
|
| 27 |
+end_res_edges <- expand_KEGG_edges(end_res_KGML, end_res_KEGG_mappings) |
|
| 28 |
+end_res_drugs <- get_drug_table("hsa01522")
|
|
| 29 |
+edges_plus_kdrug <- add_kegg_drugs(end_res_edges, end_res_KEGG_mappings, end_res_drugs) |
|
| 30 |
+} |
|
| 31 |
+ |