From: vandersm <vandersm@mail.uc.edu>
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGlincs@127388 bc3139a8-67e5-0310-9ffc-ced21a209358
Shana White authored on 14/03/2017 18:21:38
| 1 | 1 |
similarity index 95% |
| 2 | 2 |
rename from R/add_kegg_drugs.R |
| 3 | 3 |
rename to R/add_KEGG_drugs.R |
| ... | ... |
@@ -15,9 +15,9 @@ |
| 15 | 15 |
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#' end_res_drugs <- get_drug_table("hsa01522")
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-#' edges_plus_kdrug <- add_kegg_drugs(end_res_edges, end_res_KEGG_mappings, end_res_drugs) |
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+#' edges_plus_kdrug <- add_KEGG_drugs(end_res_edges, end_res_KEGG_mappings, end_res_drugs) |
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| 19 | 19 |
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-add_kegg_drugs <- function(edges, KEGG_mappings, kegg_drug_table){
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+add_KEGG_drugs <- function(edges, KEGG_mappings, kegg_drug_table){
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edges$u_ID <- paste0(edges$entry1accession,":", edges$entry2accession) |
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kegg_drug_table$u_ID <- paste0(kegg_drug_table$drug_KEGG_ID,":", kegg_drug_table$gene_id) |
| 24 | 24 |
similarity index 80% |
| 25 | 25 |
rename from man/add_kegg_drugs.Rd |
| 26 | 26 |
rename to man/add_KEGG_drugs.Rd |
| ... | ... |
@@ -1,10 +1,10 @@ |
| 1 | 1 |
% Generated by roxygen2: do not edit by hand |
| 2 |
-% Please edit documentation in R/add_kegg_drugs.R |
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-\name{add_kegg_drugs}
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-\alias{add_kegg_drugs}
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+% Please edit documentation in R/add_KEGG_drugs.R |
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+\name{add_KEGG_drugs}
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+\alias{add_KEGG_drugs}
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\title{Add edges from disease/drug tables}
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\usage{
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-add_kegg_drugs(edges, KEGG_mappings, kegg_drug_table) |
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+add_KEGG_drugs(edges, KEGG_mappings, kegg_drug_table) |
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| 8 | 8 |
} |
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\arguments{
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\item{edges}{A data.frame object obtained by using the function `expand_kegg_edges`}
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| ... | ... |
@@ -26,6 +26,6 @@ end_res_KGML <- get_KGML("hsa01522")
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| 26 | 26 |
end_res_KEGG_mappings <- expand_KEGG_mappings(end_res_KGML) |
| 27 | 27 |
end_res_edges <- expand_KEGG_edges(end_res_KGML, end_res_KEGG_mappings) |
| 28 | 28 |
end_res_drugs <- get_drug_table("hsa01522")
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-edges_plus_kdrug <- add_kegg_drugs(end_res_edges, end_res_KEGG_mappings, end_res_drugs) |
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+edges_plus_kdrug <- add_KEGG_drugs(end_res_edges, end_res_KEGG_mappings, end_res_drugs) |
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| 30 | 30 |
} |
| 31 | 31 |
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