add_KEGG_drugs: Add edges from disease/drug tables
In uc-bd2k/KEGGlincs: Visualize all edges within a KEGG pathway and overlay LINCS data [option]
Description
Usage
Arguments
Value
Examples
Description
Expand edge mappings to include drugs/drug targets
for selected pathway
Usage
1
add_KEGG_drugs(edges, KEGG_mappings, kegg_drug_table)
Arguments
edges
A data.frame object obtained by using the function 'expand_kegg_edges'
KEGG_mappings
A data.frame object obtained by using the function 'expand_kegg_mappings'
kegg_drug_table
A data.frame object obtained by using the function 'get_drug_table'
Value
A data.frame object similar to the expanded edges data frame but with additional
edges representing known drugs/drug targets
Examples
1
2
3
4
5
end_res_KGML <- get_KGML("hsa01522")
end_res_KEGG_mappings <- expand_KEGG_mappings(end_res_KGML)
end_res_edges <- expand_KEGG_edges(end_res_KGML, end_res_KEGG_mappings)
end_res_drugs <- get_drug_table("hsa01522")
edges_plus_kdrug <- add_KEGG_drugs(end_res_edges, end_res_KEGG_mappings, end_res_drugs)
uc-bd2k/KEGGlincs documentation built on May 3, 2019, 2:13 p.m.
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Description Usage Arguments Value Examples
Description
Expand edge mappings to include drugs/drug targets for selected pathway
Usage
1 | add_KEGG_drugs(edges, KEGG_mappings, kegg_drug_table)
|
Arguments
edges |
A data.frame object obtained by using the function 'expand_kegg_edges' |
KEGG_mappings |
A data.frame object obtained by using the function 'expand_kegg_mappings' |
kegg_drug_table |
A data.frame object obtained by using the function 'get_drug_table' |
Value
A data.frame object similar to the expanded edges data frame but with additional edges representing known drugs/drug targets
Examples
1 2 3 4 5 | end_res_KGML <- get_KGML("hsa01522")
end_res_KEGG_mappings <- expand_KEGG_mappings(end_res_KGML)
end_res_edges <- expand_KEGG_edges(end_res_KGML, end_res_KEGG_mappings)
end_res_drugs <- get_drug_table("hsa01522")
edges_plus_kdrug <- add_KEGG_drugs(end_res_edges, end_res_KEGG_mappings, end_res_drugs)
|
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