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Hello,
I am encountering an error when using the enrichKEGG function from the clusterProfiler package with my own created library for Klebisella pneumoniae subsp. pneumoniae HS11286 (taxid: 1125630).
Below is an example demonstrating the issue:
`library(clusterProfiler)
ids<-bitr(names(original_gene_list), fromType = "SYMBOL", toType = "ENTREZID", OrgDb=organism) # remove duplicate IDS (here I use "ENSEMBL", but it should be whatever was selected as keyType)
dedup_ids = ids[!duplicated(ids[c("SYMBOL")]),]
df2 = pstexp2[pstexp2$Gene.symbol %in% dedup_ids$SYMBOL,]
df2$Y = dedup_ids$ENTREZID
kegg_gene_list <- df2$logFC
names(kegg_gene_list) <- df2$Y
kegg_gene_list<-na.omit(kegg_gene_list)
kegg_gene_list = sort(kegg_gene_list, decreasing = TRUE)
kegg_sig_genes_df = subset(df2, df2$adj.P.Val < 0.05)
kegg_genes <- kegg_sig_genes_df$logFC
names(kegg_genes) <- kegg_sig_genes_df$Y
kegg_genes <- na.omit(kegg_genes)
kegg_genes <- names(kegg_genes)[abs(kegg_genes) > 0.05]
The following is my error message: Reading KEGG annotation online: "https://rest.kegg.jp/link/org.Kpm.eg.db/pathway"... Error in file(con, "r") : cannot open the connection to 'https://rest.kegg.jp/link/org.Kpm.eg.db/pathway' In addition: Warning message: In file(con, "r") : cannot open URL 'https://rest.kegg.jp/link/org.Kpm.eg.db/pathway': HTTP status was '400 Bad Request'
Some one could help me here please?
Best,
Roua Popescu
The text was updated successfully, but these errors were encountered:
There is a lot of (non-reproducible) code in your post, but to me it seems that when calling the enrichKEGG function the argument organism should be kegg_organism (and not organism).
Note that the URL you posted contains the OrgDb, but it should rather be the kegg organism...
Thank you for the suggestions!
Now the enrichKEGG function works.
It seems that the problem was due to the fact that the ENTREZID column had a '.0' at the end of each ENTREZ ID (I don't understand why). But, after I cleaned the ENTREZID column, the enricKEGG function worked.
Hello,
I am encountering an error when using the enrichKEGG function from the clusterProfiler package with my own created library for Klebisella pneumoniae subsp. pneumoniae HS11286 (taxid: 1125630).
Below is an example demonstrating the issue:
`library(clusterProfiler)
ids<-bitr(names(original_gene_list), fromType = "SYMBOL", toType = "ENTREZID", OrgDb=organism) # remove duplicate IDS (here I use "ENSEMBL", but it should be whatever was selected as keyType)
dedup_ids = ids[!duplicated(ids[c("SYMBOL")]),]
df2 = pstexp2[pstexp2$Gene.symbol %in% dedup_ids$SYMBOL,]
df2$Y = dedup_ids$ENTREZID
kegg_gene_list <- df2$logFC
names(kegg_gene_list) <- df2$Y
kegg_gene_list<-na.omit(kegg_gene_list)
kegg_gene_list = sort(kegg_gene_list, decreasing = TRUE)
kegg_sig_genes_df = subset(df2, df2$adj.P.Val < 0.05)
kegg_genes <- kegg_sig_genes_df$logFC
names(kegg_genes) <- kegg_sig_genes_df$Y
kegg_genes <- na.omit(kegg_genes)
kegg_genes <- names(kegg_genes)[abs(kegg_genes) > 0.05]
kegg_organism = "kpm"
kk <- enrichKEGG(gene=kegg_genes, universe=names(kegg_gene_list),organism=organism, pvalueCutoff = 0.05, keyType = "ncbi-geneid")`
The following is my error message:
Reading KEGG annotation online: "https://rest.kegg.jp/link/org.Kpm.eg.db/pathway"... Error in file(con, "r") : cannot open the connection to 'https://rest.kegg.jp/link/org.Kpm.eg.db/pathway' In addition: Warning message: In file(con, "r") : cannot open URL 'https://rest.kegg.jp/link/org.Kpm.eg.db/pathway': HTTP status was '400 Bad Request'
Some one could help me here please?
Best,
Roua Popescu
The text was updated successfully, but these errors were encountered: