Browse code

modify drug table output

From: vandersm <vandersm@mail.uc.edu>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGlincs@126896 bc3139a8-67e5-0310-9ffc-ced21a209358

Shana White authored on 22/02/2017 20:49:03
Showing 2 changed files

... ...
@@ -8,6 +8,7 @@ export(expand_KEGG_edges)
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 export(expand_KEGG_mappings)
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 export(generate_mappings)
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 export(get_KGML)
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+export(get_drug_table)
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 export(get_fisher_info)
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 export(get_graph_object)
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 export(node_mapping_info)
... ...
@@ -21,6 +21,26 @@ get_drug_table <- function(pathwayid){
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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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+        names(d_table) <- c("drug_KEGG_ID", "drug_name", "gene_target")
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+        d_table$gene_target <- strsplit(d_table$gene_target, " ")
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+
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+        for(i in 1:nrow(d_table)){
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+            l <- length(unlist(d_table$gene_target[i]))
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+            d_table$drug_KEGG_ID[i] <- list(rep(d_table$drug_KEGG_ID[i], l))
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+            d_table$drug_name[i] <- list(rep(d_table$drug_name[i], l))
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+        }
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+        
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+        long_drug <- data.frame("drug_KEGG_ID" = unlist(d_table$drug_KEGG_ID), 
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+                                "drug_name" = unlist(d_table$drug_name), 
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+                                "gene_target" = unlist(d_table$gene_target),
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+                                 stringsAsFactors = FALSE)
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+        for (i in 1:nrow(long_drug)){
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+            long_drug$gene_id[i] <- strsplit(long_drug$gene_target[i], "\\(")[[1]][1]
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+            long_drug$gene_symbol[i] <- regmatches(long_drug$gene_target[i], gregexpr("(?<=\\().*?(?=\\))", long_drug$gene_target[i], perl=T))[[1]]
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+        }
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+        drops <- "gene_target"
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+        d_table <- long_drug[, names(long_drug) != drops]
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+        
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         return(d_table)
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     }
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     else {