function gson doesn't properly handle the keytype argument

[guidohooiveld]

At the clusterProfiler GitHub an error was reported that originates from an 'incomplete' GSON object.
See: YuLab-SMU/clusterProfiler#685 (comment)

I did some debugging, and found that it seems to originate from the gson function, hence my post here. Somehow the slot keytype remains empty, although a value for it is being provided.

@GuangchuangYu : could please have a look at this?

gson/R/gson.R

Lines 27 to 29 in 519e148

	gson <- function(gsid2gene, gsid2name = NULL, gene2name = NULL,
	species = NULL, gsname = NULL, version = NULL,
	accessed_date = NULL, keytype = NULL, urlpattern = NULL, info = NULL) {

Code illustrating problem (as per post at the clusterProfiler GitHub)

> ## load library
> library(clusterProfiler)
> 
> ## some ids
> id_transform <- c("240427","12705","241770","102633301","319757","116903","72309")
> 
> ## generate GSON-object with pathway information
> kk <- gson_KEGG('mmu')
> 
> ## use GSON as input: FAILS!
> KEGG_enrich = enrichKEGG(gene = id_transform,
+                          organism=kk,
+                          use_internal_data = FALSE)
Error in (function (cl, name, valueClass)  : 
  assignment of an object of class “NULL” is not valid for @‘keytype’ in an object of class “enrichResult”; is(value, "character") is not TRUE
> 
> 
> ## check GSON-object
> kk
>> Gene Set: KEGG
>> 9710 genes annotated by 355 gene sets.
>> Species: mmu
>> Version: Release 110.0+/04-27, Apr 24
> 
> ## note that slot keytype is NULL!
> str(kk)
Formal class 'GSON' [package "gson"] with 9 slots
  ..@ gsid2gene    :'data.frame':       38640 obs. of  2 variables:
  .. ..$ gsid: chr [1:38640] "mmu00010" "mmu00010" "mmu00010" "mmu00010" ...
  .. ..$ gene: chr [1:38640] "103988" "106557" "110695" "11522" ...
  ..@ gsid2name    :'data.frame':       355 obs. of  2 variables:
  .. ..$ gsid: chr [1:355] "mmu01100" "mmu01200" "mmu01210" "mmu01212" ...
  .. ..$ name: chr [1:355] "Metabolic pathways - Mus musculus (house mouse)" "Carbon metabolism - Mus musculus (house mouse)" "2-Oxocarboxylic acid metabolism - Mus musculus (house mouse)" "Fatty acid metabolism - Mus musculus (house mouse)" ...
  ..@ gene2name    : NULL
  ..@ species      : chr "mmu"
  ..@ gsname       : chr "KEGG"
  ..@ version      : chr "Release 110.0+/04-27, Apr 24"
  ..@ accessed_date: chr "2024-04-30"
  ..@ keytype      : NULL
  ..@ info         : NULL
> 

Perform some debugging
debug function gson_kegg

https://github.com/YuLab-SMU/clusterProfiler/blob/2ab30a92f1791dce75f71ea29b71c33fc443d4a0/R/gson.R#L12-L25

> library(clusterProfiler)
> library(gson)
> 
> ## define unexposed help function 'kegg_release'
> ## https://github.com/YuLab-SMU/clusterProfiler/blob/2ab30a92f1791dce75f71ea29b71c33fc443d4a0/R/gson.R#L285-L289
> kegg_release = function(db){
+   url = paste0("https://rest.kegg.jp/info/", db)
+   y = readLines(url)
+   release <- sub("\\w+\\s+", "", y[grep('Release', y)])
+   return(release) }
> 
> ## define required arguments
> species = 'hsa'
> KEGG_Type="KEGG"
> keyType="kegg"
> 
> ## run code (as per function gson_kegg)
> x <- download_KEGG(species, KEGG_Type, keyType)
Reading KEGG annotation online: "https://rest.kegg.jp/link/hsa/pathway"...
Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/hsa"...
> gsid2gene <- setNames(x[[1]], c("gsid", "gene"))
> gsid2name <- setNames(x[[2]], c("gsid", "name"))
> version <- kegg_release(species)
> 
> ## create GSON-object
> My.GSON <-gson(gsid2gene = gsid2gene, 
+                gsid2name = gsid2name,
+                species = species,
+                gsname = "KEGG",
+                version = version,
+                accessed_date = as.character(Sys.Date(),
+                keytype = "ENTREZID")
+                )
> 
> 
> ## check
> ## Note that slot keytype = NULL! And not "ENTREZID".
> str(My.GSON)
Formal class 'GSON' [package "gson"] with 9 slots
  ..@ gsid2gene    :'data.frame':       36987 obs. of  2 variables:
  .. ..$ gsid: chr [1:36987] "hsa00010" "hsa00010" "hsa00010" "hsa00010" ...
  .. ..$ gene: chr [1:36987] "10327" "124" "125" "126" ...
  ..@ gsid2name    :'data.frame':       359 obs. of  2 variables:
  .. ..$ gsid: chr [1:359] "hsa01100" "hsa01200" "hsa01210" "hsa01212" ...
  .. ..$ name: chr [1:359] "Metabolic pathways" "Carbon metabolism" "2-Oxocarboxylic acid metabolism" "Fatty acid metabolism" ...
  ..@ gene2name    : NULL
  ..@ species      : chr "hsa"
  ..@ gsname       : chr "KEGG"
  ..@ version      : chr "Release 110.0+/04-28, Apr 24"
  ..@ accessed_date: chr "2024-04-30"
  ..@ keytype      : NULL
  ..@ info         : NULL
> 

[guidohooiveld]

@GuangchuangYu : I noticed on the GitHub pages that during the last days you are actively working on a variety of your projects. Therefore a kind reminder to 'squash this bug' as well. :)