use use_KEGGREST function

R/overlap_coefficient.R

@@ -96,10 +96,10 @@ overlap_coefficient <- function(pathwayA, pathwayB, pathways = NULL, organism =
       }
       
       code <- substr(pathwayA, start = 1, stop = nchar(pathwayA) - 5)
-      kegg_org <- KEGGREST::keggList("organism")
+      kegg_org <- use_KEGGREST(KEGGREST::keggList("organism"))
       
       if (!code %in% kegg_org) {
-        pathlist <- KEGGREST::keggList("pathway", organism)
+        pathlist <- use_KEGGREST(KEGGREST::keggList("pathway", organism))
         pathlist <- as.data.frame(pathlist)
         pathlist$pathway_code <- rownames(pathlist)
         
@@ -112,7 +112,7 @@ overlap_coefficient <- function(pathwayA, pathwayB, pathways = NULL, organism =
         pathwayB <- pathlist[pathlist$pathlist == pathwayB, "pathway_code"]
       }
       
-      pathinfo <- KEGGREST::keggGet(c(pathwayA, pathwayB))
+      pathinfo <- use_KEGGREST(KEGGREST::keggGet(c(pathwayA, pathwayB)))
       A <- pathinfo[[1]]$COMPOUND
       B <- pathinfo[[2]]$COMPOUND
     }

R/pathway_search.R

@@ -53,7 +53,7 @@ pathway_search <- function(metab, organism, min_size = 2) {
   if (!is.character(organism) & !length(organism) == 1) {
     stop("`organism` must be a character.")
   }
-  kegg_org <- KEGGREST::keggList("organism")
+  kegg_org <- use_KEGGREST(KEGGREST::keggList("organism"))
   kegg_org <- as.data.frame(kegg_org)
   
   if (!(organism %in% kegg_org$organism)) {
@@ -63,7 +63,7 @@ pathway_search <- function(metab, organism, min_size = 2) {
   message("Starts searching for pathways...")
   
   # search KEGG pathways
-  pathlist <- KEGGREST::keggList("pathway", organism)
+  pathlist <- use_KEGGREST(KEGGREST::keggList("pathway", organism))
   pathlist <- as.data.frame(pathlist)
   colnames(pathlist) <- "pathway_name"
   pathlist <- rownames_to_column(pathlist, "pathway_code")
@@ -74,7 +74,8 @@ pathway_search <- function(metab, organism, min_size = 2) {
                                 fixed = TRUE)
   
   comp <- sapply(1:nrow(pathlist), function(i) {
-    path <- KEGGREST::keggGet(paste0("path:", pathlist$pathway_code[i]))
+    path <- use_KEGGREST(KEGGREST::keggGet(paste0("path:",
+                                                  pathlist$pathway_code[i])))
     path <- as.data.frame(path[[1]]$COMPOUND)
   })
   names(comp) <- pathlist$pathway_code

R/test_pathway.R

@@ -138,7 +138,7 @@ test_pathway <- function(quantif, design, pathways = "auto", fixed, random,
       stop("Package 'KEGGREST' not available. Automatic pathway searching", 
            " cannot be performed.")
     }
-    kegg_org <- KEGGREST::keggList("organism")
+    kegg_org <- use_KEGGREST(KEGGREST::keggList("organism"))
     kegg_org <- as.data.frame(kegg_org)
     kegg_org <- unique(kegg_org$organism)