KEGG patwhay analysis

Question

[bookorg]

I faced a problem for analyzing my KEGG pathway from the DEG that i have found by analyzing SARS-COV2 GEO database.

kk2 <- gseKEGG(geneList     = geneList,
               organism     = 'hsa',
               nPerm        = 1000,
               minGSSize    = 120,
               pvalueCutoff = 0.05,
               verbose      = FALSE)
head(summary(kk2))

this is the code but the problem is i am unable to track hsa,that means organism.Is this a R package like org.Hs.eg.db,if so can anyone give the link of that plz.So that i can install it in R and able to run my code.THANKS

[seidel]

Have you tried searching for the package? First google hit: https://bioconductor.org/packages/release/data/annotation/html/org.Hs.eg.db.html

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("org.Hs.eg.db")

However, I don't think this is the source of your problem. What error are you getting? Have you tried the minimal example from the package? (try the test data set and remove the nPerm argument). If you get success with that, but not your geneList, it implies something is off with your geneList.

library(clusterProfiler)
data(geneList, package="DOSE")
kk2 <- gseKEGG(geneList     = geneList,
               organism     = 'hsa',
               minGSSize    = 120,
               pvalueCutoff = 0.05,
               verbose      = FALSE)

[bookorg]

I have this package,but for KEGG analysis ,this doesnot work.something called hsa should be their

[jv]

what exactly is the error that you get when running the code from your question? It is very difficult to troubleshoot without specific error information.

[bookorg]

1.KK <- gseKEGG(sign_DEG_GSE147507_LogFC)

2.KK <- setReadable(KK, org.Hs.eg.db)

3.KK@result$Description <- str_to_title(str_wrap(KK@result$Description, 50)) I ran that code for KEGG pathway analysis of my DEG.both 1 and 3 ran well but i am unable to run code no 2.When I ran the 2 no code ,in consol the below comments are written KK <- gseKEGG(sign_DEG_GSE147507_LogFC)

[Error in setReadable(KK, org.Hs.eg.db) : can't determine keyType automatically; need to set 'keyType' explicitly...] thats my problem,why this appears.

[jv]

according to documentation for clusterProfiler::gseKEGG the keyType parameters is by default set to "kegg" which means gseKEGG is expecting the gene names in geneList to be KEGG gene identifiers. That you get this error indicates that the gene identifiers in geneList are something other than KEGG. You have additional options for keyType such as 'ncbi-geneid', 'ncib-proteinid' and 'uniprot'. You will need to set this parameters to match the gene identifiers that you are using so long as it is one of the four options allowed by the function. Kudos to @seidel who likewise suggested that something is likely off with your gene list.

[bookorg]

Thanks for the suggestion.But without the 2no code ,I can able to run the data and found the plot.So in that way without running of second code is my generated plot are right ??

[jv]

Sorry for not looking at your code example closely enough, but the issue with setReadable is still with the gene keyType. From the setReadable code you can see that keyType is being pulled from your KK object and returning as "UNKNOWN" leading to the error that you are getting:

if (keyType == "auto") {
    keyType <- x@keytype
    if (keyType == 'UNKNOWN') {
        stop("can't determine keyType automatically; need to set 'keyType' explicitly...")
    }
}

Since it looks like you are running gseKEGG with the default keyType param then my guess would be that the gene identifiers in KK are KEGG identifiers but I'm not sure why setReadable doesn't recognize that but it may be that setReadable doesn't support KEGG identifiers.

If you use Entrez gene ids for for your gene list when running gseKEGG do you get this same error from setReadable?

[bookorg]

Yes I have used entrezid and already able to generate GO and reactome and wiki plot .For all this setreadable work properly except for KEGG.As i am working by human gene ,so my annotation db- should be org.Hs.eg.db for GO,reactome and wiki.But KEGG there should be hsa except org,hs,eg.db.But i dont know why this appears.