add_edge_data: Annotate KEGG edge mappings with user data

In uc-bd2k/KEGGlincs: Visualize all edges within a KEGG pathway and overlay LINCS data [option]

Description

Add data column[s] to object created from function expand_KEGG_edges

Usage

add_edge_data(expanded_edges, KEGG_mappings, user_data, map_type = "SYMBOL",
  data_column_no = 3, only_mapped = FALSE)

Arguments

expanded_edges	The data frame object generated via the function expand_KEGG_edges
KEGG_mappings	KEGG_mappings The data.frame object generated by the function expand_KEGG_mappings
user_data	A data frame where in which the first two columns contain gene symbols representing an edge and any/all other column[s] contain corresponding edge data.
map_type	If the genes in your data set are left untranslated set to "NUMBER" (assuming numbers are gene accession numbers)
data_column_no	The column index for desired user data to be added
only_mapped	A logical indicator; if set to FALSE will return 'de-novo' edges that 'exist' in data but are not documented in KEGG

Value

A data frame object with detailed KEGG edge mappings annotated with user data

Examples

p53_KGML <- get_KGML('hsa04115')
p53_KEGG_mappings <- expand_KEGG_mappings(p53_KGML)
p53_edges <- expand_KEGG_edges(p53_KGML, p53_KEGG_mappings)
p53_HA1E_data <- overlap_info(p53_KGML, p53_KEGG_mappings, 'HA1E', 
                               data_type = '100_bing', only_mapped = FALSE)
                               
p53_edges_HA1E_ALL <- add_edge_data(p53_edges, p53_KEGG_mappings, 
                                     p53_HA1E_data, c(3, 10,12))
p53_edges_HA1E_MAPPED <- add_edge_data(p53_edges, p53_KEGG_mappings, 
                                        p53_HA1E_data, c(3, 10,12), 
                                        only_mapped = TRUE)

uc-bd2k/KEGGlincs documentation built on May 3, 2019, 2:13 p.m.