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
... | ... |
@@ -21,6 +21,26 @@ get_drug_table <- function(pathwayid){ |
21 | 21 |
warning("No associated drug targets in selected pathway") |
22 | 22 |
return() |
23 | 23 |
} |
24 |
+ names(d_table) <- c("drug_KEGG_ID", "drug_name", "gene_target") |
|
25 |
+ d_table$gene_target <- strsplit(d_table$gene_target, " ") |
|
26 |
+ |
|
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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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+ |
|
24 | 44 |
return(d_table) |
25 | 45 |
} |
26 | 46 |
else { |