How to resolve the following error in obtainedgelist ?

[Poovizhi]

Hi, please help me in resolving the following error
Error in checkIDs(genes, metabolites) :
The following IDs were not found in the keylist and thus are not able to be converted:
ENTREZID: 58003, 797319, 561370, 567205, 570167, 560802...
This error I got when using obtainedgelist for daniorerio entrezid from kegg and reactome.

[nirgrahamuk]

Hi, welcome!

We don't really have enough info to help you out. Could you ask this with a minimal REPRoducible EXample (reprex)? A reprex makes it much easier for others to understand your issue and figure out how to help.

If you've never heard of a reprex before, you might want to start by reading this FAQ:

FAQ: How to do a minimal reproducible example ( reprex ) for beginners

A minimal reproducible example consists of the following items: A minimal dataset, necessary to reproduce the issue The minimal runnable code necessary to reproduce the issue, which can be run on the given dataset, and including the necessary information on the used packages. Let's quickly go over each one of these with examples: Minimal Dataset (Sample Data) You need to provide a data frame that is small enough to be (reasonably) pasted on a post, but big enough to reproduce your issue. Let's say, as an example, that you are working with the iris data frame head(iris) #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> 1 5.1 3.5 1.4 0.…

[Poovizhi]

AnnotationDbi::keytypes(org.Dr.eg.db::org.Dr.eg.db)
#> 
#>  [1] "ACCNUM"       "ALIAS"        "ENSEMBL"      "ENSEMBLPROT"  "ENSEMBLTRANS"
#>  [6] "ENTREZID"     "ENZYME"       "EVIDENCE"     "EVIDENCEALL"  "GENENAME"    
#> [11] "GO"           "GOALL"        "IPI"          "ONTOLOGY"     "ONTOLOGYALL" 
#> [16] "PATH"         "PFAM"         "PMID"         "PROSITE"      "REFSEQ"      
#> [21] "SYMBOL"       "UNIPROT"      "ZFIN"
  head(rownames(Y))
#> Error in rownames(Y): object 'Y' not found
  table(group1)
#> Error in table(group1): object 'group1' not found
  paths <- graphite::pathways('drerio','kegg')
  paths[[1]]
#> "Glycolysis / Gluconeogenesis" pathway
#> Native ID       = dre:00010
#> Database        = KEGG
#> Species         = drerio
#> Number of nodes = 107
#> Number of edges = 1619
#> Retrieved on    = 22-04-2022
#> URL             = http://www.kegg.jp/kegg-bin/show_pathway?org_name=dre&mapno=00010
  head(nodes(paths[[1]]))
#> Error in nodes(paths[[1]]): could not find function "nodes"
  pathways_mat[1:5,7, drop = FALSE]
#> Error in eval(expr, envir, enclos): object 'pathways_mat' not found
  library(netgsa)
  
  database_search <- obtainEdgeList(rownames(Y),c("kegg","reactome"))
#> Error in rownames(Y): object 'Y' not found

^{Created on 2022-08-29 by the reprex package (v2.0.1)}

@Poovizhi

Hi, please help me in resolving the following error
Error in checkIDs(genes, metabolites) :
The following IDs were not found in the keylist and thus are not able to be converted:
ENTREZID: 58003, 797319, 561370, 567205, 570167, 560802...
This error I got when using obtainedgelist for daniorerio entrezid from kegg and reactome.