I am trying to run a KEGG enrichment analysis on my data. My genes are in SYMBOL, which I converted to ENTREZID, but I need them in "kegg" or "ncbi-geneID" to run enrichKEGG. I looked for packages that would convert these, but they are not updated: MS_convertGene, keggConv, KEGGREST, topGO.
What worked was using the website: https://www.genome.jp/kegg/tool/conv_id.html But I have many gene lists to be converted.....
Is there any tool that I could use in R to convert these IDs in a more handy way?
Thank you. Laia
Thank you for your quick reply. Then if they match, I don't get any mapping. This is my code:
And this is the error message:
Reading KEGG annotation online:
No gene can be mapped... Expected input gene ID:
Warning messages: 1: In utils::download.file(url, quiet = TRUE, method = method, ...) : the 'wininet' method is deprecated for http:// and https:// URLs 2: In utils::download.file(url, quiet = TRUE, method = method, ...) : the 'wininet' method is deprecated for http:// and https:// URLs
Maybe it is important to mention that my gene list is 424 genes long? Could that be an issue?
Thank you. Laia
Please show the output from
entrez_genes[1:10]; thus (for example) the first 10 symbols resp. entrezids.
Oops. Could it be that, because the "entrez_genes" vector is named with the symbol names, that then is not working?
Yep, that is the reason!
This is working (note the use of
as.character(), and that in the code below no significance cutoff is applied):
I keep getting the same NULL error..
'select()' returned 1:1 mapping between keys and columns
 "340206" "3598" "4319" NA "648947" NA "3589" "105369893"  NA NA
--> No gene can be mapped.... --> Expected input gene ID: --> return NULL...
Should I remove all NA? -- Nope, this did not work neither.
Also, how come you get less NA than I do?
Yours:  "340206" "3598" "4319" "124907722" "648947" "124903970"  "3589" "105369893" NA "124905027"
Mine:  "340206" "3598" "4319" NA "648947" NA
 "3589" "105369893" NA NA
NAin your vector will work.
I did notice that I retrieved only a single
NA(8th position), but you got 4. My Bioconductor installation is up-to-date (v3.16, note this version id in that of
org.Hs.eg.db), so this suggests you Bioconductor/package installation is not. Please check, and update if needed.
My clusterProfiler and org.Hs packages are the ones outdated, compared to yours. But when I run "check for package updates" it says it is up to date.... I'll update them and try again. Thanks!
BiocManager::install(version = "3.16").
The packages are (apparently) up-to-date within Bioconductor version 3.15...
I managed installing the 3.16 version of BiocManager. R said there were 91 packages to be updated, so I did. However, some warning messages appeared. One example:
Now, if I ask what version I have for the two packages (cluster and org), they are the same as yours. But I fail to call their libraries. I get this error:
Is it ok that the downloaded packages are all going to a Temp folder?
Other warning messages:
This part is the main issue.
You should restart R and then re-install
I could finally solve this and I could get KEGG results :) Thank you so much for your help and quick replies.