KEGG

[enluo211]

##code
library(AnnotationHub)
library(rlang)
require(clusterProfiler)
#bitr(keys(maize)[1], 'ENTREZID', c("REFSEQ", "GO", "ONTOLOGY"), maize)
gene<-read.table("gene.txt",header=FALSE)
require(DOSE)
gene<-as.character(gene[,1])
ekk <- enrichKEGG(gene,organism = "zma",pAdjustMethod = "BH",pvalueCutoff = 0.05,use_internal_data = F)
##error
fail to download KEGG data...
Error in download.KEGG.Path(species) :
'species' should be one of organisms listed in 'http://www.genome.jp/kegg/catalog/org_list.html'...
Calls: enrichKEGG ... prepare_KEGG -> download_KEGG -> download.KEGG.Path
In addition: Warning message:
In utils::download.file(url, quiet = quiet, method = "libcurl", :
URL 'https://rest.kegg.jp/link/zma/pathway': status was 'Failure when receiving data from the peer'
##code
devtools::install_github("YuLab-SMU/createKEGGdb",force = TRUE)
library(createKEGGdb)
createKEGGdb::create_kegg_db(organism = "zma")
##error
Error in createKEGGdb::create_kegg_db(organism = "zma") :
unused argument (organism = "zma")
I can not understand,Can you help me?

[guidohooiveld]

Based on what you posted it seems that the KEGG website could not be connected to. Maybe it was a temporary hick-up?

Using some random maize entrezids (and pvalueCutoff = 1):

> library(clusterProfiler)
> 
> gene <- c("541983", "542523", "100283318", "732839", "542214", "541670", "541612")
> 
> ekk <- enrichKEGG(gene, organism = "zma",pAdjustMethod = "BH", pvalueCutoff = 1)
Reading KEGG annotation online: "https://rest.kegg.jp/link/zma/pathway"...
Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/zma"...
> 
> ekk
#
# over-representation test
#
#...@organism    zma 
#...@ontology    KEGG 
#...@keytype     kegg 
#...@gene        chr [1:7] "541983" "542523" "100283318" "732839" "542214" "541670" ...
#...pvalues adjusted by 'BH' with cutoff <1 
#...8 enriched terms found
'data.frame':   8 obs. of  14 variables:
 $ category      : chr  "Metabolism" "Metabolism" "Metabolism" "Metabolism" ...
 $ subcategory   : chr  "Amino acid metabolism" "Energy metabolism" "Metabolism of other amino acids" "Amino acid metabolism" ...
 $ ID            : chr  "zma00220" "zma00910" "zma00410" "zma00330" ...
 $ Description   : chr  "Arginine biosynthesis" "Nitrogen metabolism" "beta-Alanine metabolism" "Arginine and proline metabolism" ...
 $ GeneRatio     : chr  "1/4" "1/4" "1/4" "1/4" ...
 $ BgRatio       : chr  "41/9509" "43/9509" "47/9509" "61/9509" ...
 $ RichFactor    : num  0.0244 0.0233 0.0213 0.0164 0.0149 ...
 $ FoldEnrichment: num  58 55.3 50.6 39 35.5 ...
 $ zScore        : num  7.5 7.32 6.99 6.1 5.81 ...
 $ pvalue        : num  0.0171 0.018 0.0196 0.0254 0.0279 ...
 $ p.adjust      : num  0.0446 0.0446 0.0446 0.0446 0.0446 ...
 $ qvalue        : num  0.0117 0.0117 0.0117 0.0117 0.0117 ...
 $ geneID        : chr  "542214" "542214" "541983" "541983" ...
 $ Count         : int  1 1 1 1 1 1 1 1
#...Citation
G Yu. Thirteen years of clusterProfiler. The Innovation. 2024, 5(6):100722 

> as.data.frame(ekk)
           category                     subcategory       ID
zma00220 Metabolism           Amino acid metabolism zma00220
zma00910 Metabolism               Energy metabolism zma00910
zma00410 Metabolism Metabolism of other amino acids zma00410
zma00330 Metabolism           Amino acid metabolism zma00330
zma00250 Metabolism           Amino acid metabolism zma00250
zma00630 Metabolism         Carbohydrate metabolism zma00630
zma00195 Metabolism               Energy metabolism zma00195
zma01230 Metabolism        Global and overview maps zma01230
                                         Description GeneRatio  BgRatio
zma00220                       Arginine biosynthesis       1/4  41/9509
zma00910                         Nitrogen metabolism       1/4  43/9509
zma00410                     beta-Alanine metabolism       1/4  47/9509
zma00330             Arginine and proline metabolism       1/4  61/9509
zma00250 Alanine, aspartate and glutamate metabolism       1/4  67/9509
zma00630     Glyoxylate and dicarboxylate metabolism       1/4 113/9509
zma00195                              Photosynthesis       1/4 146/9509
zma01230                 Biosynthesis of amino acids       1/4 293/9509
          RichFactor FoldEnrichment   zScore     pvalue   p.adjust     qvalue
zma00220 0.024390244      57.981707 7.500613 0.01713828 0.04462673 0.01174388
zma00910 0.023255814      55.284884 7.318607 0.01796862 0.04462673 0.01174388
zma00410 0.021276596      50.579787 6.989734 0.01962772 0.04462673 0.01174388
zma00330 0.016393443      38.971311 6.103080 0.02541802 0.04462673 0.01174388
zma00250 0.014925373      35.481343 5.810160 0.02789170 0.04462673 0.01174388
zma00630 0.008849558      21.037611 4.395539 0.04670054 0.06226739 0.01638615
zma00195 0.006849315      16.282534 3.817357 0.06002473 0.06859969 0.01805255
zma01230 0.003412969       8.113481 2.537133 0.11768886 0.11768886 0.03097075
         geneID Count
zma00220 542214     1
zma00910 542214     1
zma00410 541983     1
zma00330 541983     1
zma00250 542214     1
zma00630 542214     1
zma00195 541612     1
zma01230 542214     1
> 

[enluo211]

I updated the version of R and reinstalled the R packages. The problem has been solved.

…

------------------&nbsp;原始邮件&nbsp;------------------ 发件人: "YuLab-SMU/clusterProfiler" ***@***.***&gt;; 发送时间:&nbsp;2025年7月21日(星期一) 下午4:29 ***@***.***&gt;; ***@***.******@***.***&gt;; 主题:&nbsp;Re: [YuLab-SMU/clusterProfiler] KEGG (Issue #780) guidohooiveld left a comment (YuLab-SMU/clusterProfiler#780) Based on what you posted it seems that the KEGG website could not be connected to. Maybe it was a temporary hick-up? Using some random maize entrezids (and pvalueCutoff = 1): &gt; library(clusterProfiler) &gt; &gt; gene <- c("541983", "542523", "100283318", "732839", "542214", "541670", "541612") &gt; &gt; ekk <- enrichKEGG(gene, organism = "zma",pAdjustMethod = "BH", pvalueCutoff = 1) Reading KEGG annotation online: "https://rest.kegg.jp/link/zma/pathway"... Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/zma"... &gt; &gt; ekk # # over-representation test # ***@***.*** zma ***@***.*** KEGG ***@***.*** kegg ***@***.*** chr [1:7] "541983" "542523" "100283318" "732839" "542214" "541670" ... #...pvalues adjusted by 'BH' with cutoff <1 #...8 enriched terms found 'data.frame': 8 obs. of 14 variables: $ category : chr "Metabolism" "Metabolism" "Metabolism" "Metabolism" ... $ subcategory : chr "Amino acid metabolism" "Energy metabolism" "Metabolism of other amino acids" "Amino acid metabolism" ... $ ID : chr "zma00220" "zma00910" "zma00410" "zma00330" ... $ Description : chr "Arginine biosynthesis" "Nitrogen metabolism" "beta-Alanine metabolism" "Arginine and proline metabolism" ... $ GeneRatio : chr "1/4" "1/4" "1/4" "1/4" ... $ BgRatio : chr "41/9509" "43/9509" "47/9509" "61/9509" ... $ RichFactor : num 0.0244 0.0233 0.0213 0.0164 0.0149 ... $ FoldEnrichment: num 58 55.3 50.6 39 35.5 ... $ zScore : num 7.5 7.32 6.99 6.1 5.81 ... $ pvalue : num 0.0171 0.018 0.0196 0.0254 0.0279 ... $ p.adjust : num 0.0446 0.0446 0.0446 0.0446 0.0446 ... $ qvalue : num 0.0117 0.0117 0.0117 0.0117 0.0117 ... $ geneID : chr "542214" "542214" "541983" "541983" ... $ Count : int 1 1 1 1 1 1 1 1 #...Citation G Yu. Thirteen years of clusterProfiler. The Innovation. 2024, 5(6):100722 &gt; as.data.frame(ekk) category subcategory ID zma00220 Metabolism Amino acid metabolism zma00220 zma00910 Metabolism Energy metabolism zma00910 zma00410 Metabolism Metabolism of other amino acids zma00410 zma00330 Metabolism Amino acid metabolism zma00330 zma00250 Metabolism Amino acid metabolism zma00250 zma00630 Metabolism Carbohydrate metabolism zma00630 zma00195 Metabolism Energy metabolism zma00195 zma01230 Metabolism Global and overview maps zma01230 Description GeneRatio BgRatio zma00220 Arginine biosynthesis 1/4 41/9509 zma00910 Nitrogen metabolism 1/4 43/9509 zma00410 beta-Alanine metabolism 1/4 47/9509 zma00330 Arginine and proline metabolism 1/4 61/9509 zma00250 Alanine, aspartate and glutamate metabolism 1/4 67/9509 zma00630 Glyoxylate and dicarboxylate metabolism 1/4 113/9509 zma00195 Photosynthesis 1/4 146/9509 zma01230 Biosynthesis of amino acids 1/4 293/9509 RichFactor FoldEnrichment zScore pvalue p.adjust qvalue zma00220 0.024390244 57.981707 7.500613 0.01713828 0.04462673 0.01174388 zma00910 0.023255814 55.284884 7.318607 0.01796862 0.04462673 0.01174388 zma00410 0.021276596 50.579787 6.989734 0.01962772 0.04462673 0.01174388 zma00330 0.016393443 38.971311 6.103080 0.02541802 0.04462673 0.01174388 zma00250 0.014925373 35.481343 5.810160 0.02789170 0.04462673 0.01174388 zma00630 0.008849558 21.037611 4.395539 0.04670054 0.06226739 0.01638615 zma00195 0.006849315 16.282534 3.817357 0.06002473 0.06859969 0.01805255 zma01230 0.003412969 8.113481 2.537133 0.11768886 0.11768886 0.03097075 geneID Count zma00220 542214 1 zma00910 542214 1 zma00410 541983 1 zma00330 541983 1 zma00250 542214 1 zma00630 542214 1 zma00195 541612 1 zma01230 542214 1 &gt; — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***&gt;