corrections to the function

Integration/MINERVA_access/minerva_access_functions.R

@@ -80,11 +80,11 @@ get_annotation <- function(references, selected_type) {
 }
 
 ### A function retrieving element identifiers from a given MINERVA element set
-get_component_annotations <- function(components, annotation_type) {
+get_components_annotations <- function(components, annotation_type) {
   ### Get MINERVA references as a named list
   message(paste0("Retrieving ", annotation_type, "identifiers for this MINERVA collection"))
   ### Apply get_annotation function
-  mnv_refs <- sapply(fcomponents$map_elements, function(x) sapply(x$references, get_annotation, annotation_type) )
-  names(mnv_refs) <- fcomponents$models$name
+  mnv_refs <- sapply(components$map_elements, function(x) sapply(x$references, get_annotation, annotation_type) )
+  names(mnv_refs) <- components$models$name
   return(mnv_refs)
 }
\ No newline at end of file

Resources/Crosstalks/find_crosstalks.R

@@ -36,15 +36,6 @@ get_reactome_pathway_contents <- function(reactome_path_id) {
   return(unlist(unique(symbols)))
 }
 
-### A function retrieving element identifiers from MINERVA
-get_mnv_refs <- function(fcomponents) {
-  ### Get MINERVA HGNCs as a named list
-  message("Retrieving MINERVA HGNCs collection")
-  mnv_refs <- sapply(fcomponents$map_elements, function(x) sapply(x$references, get_annotation, "HGNC_SYMBOL") )
-  names(mnv_refs) <- fcomponents$models$name
-  return(mnv_refs)
-}
-
 ### A function retrieving element identifiers from WikiPathway diagrams 
 get_wp_refs <- function() {
   message("Retrieving WP collection")
@@ -174,7 +165,7 @@ map_components <- get_map_components(map)
 map_groups <- fromJSON("map_groups.json")
 
 ### Detailed lists
-mnv_refs <- get_mnv_refs(map_components)
+mnv_refs <- get_component_annotations(map_components, "HGNC_SYMBOL")
 wp_refs <- get_wp_refs()
 rct_refs <- get_rct_refs()