Hello, im struggling to load my data into topGo. I have been able to load in the preinstalled data but when i try my own i get the error

Error in split.default(names(sort(nl)), f.index): first argument must be a vector

I have found some similar post/problems but i still cannot identify the issue.

Im bringing over gene lists and p values from a DESEQ2 output and loading that as a genelist, along with a GO file for my organism as follows;

# extract the adjusted p-values from  our results object
geneList <- res$padj

# add the gene names from our results to our list of adjusted p-values
names(geneList) <- rownames(res)

# remove genes with an adjusted p-value recorded as NA
geneList<-na.omit(geneList)

#load in GO data from B.imp
geneID2GO <- readMappings(file = "Bombus_impatiens_BP_All.txt", IDsep = ",", sep = "\t")
sessionInfo( )

these data look like;

but when i run topGo, i get the error

sampleGOdata <- new("topGOdata",
              ontology = "BP", 
             allGenes = geneList,
              geneSel = topDiffGenes,
              nodeSize = 10,
              annot = annFUN.gene2GO, 
              gene2GO = geneID2GO
                   )

Building most specific GOs .....

    ( 0 GO terms found. )


Build GO DAG topology ..........

    ( 0 GO terms and 0 relations. )

Nothing to do:

Error in split.default(names(sort(nl)), f.index): first argument must be a vector
Traceback:

1. new("topGOdata", ontology = "BP", allGenes = geneList, geneSel = topDiffGenes, 
 .     nodeSize = 10, annot = annFUN.gene2GO, gene2GO = geneID2GO)
2. initialize(value, ...)
3. initialize(value, ...)
4. .local(.Object, ...)
5. buildLevels(g, leafs2root = TRUE)
6. split(names(sort(nl)), f.index)
7. split.default(names(sort(nl)), f.index)

Based on other posts i thought maybe my genelist file wasnt a vector but;

typeof(geneList)
'double'

And if i run

v.geneList <- as.vector(geneList,'numeric')

sessionInfo( )

and put that through, i still get the error.

Could it be the geneID2GO file? the format looks like it should so im pretty stumped! Any suggestions appreciated!

Realised the issue, i needed to use IDsep = ";" when loading the GO data;

#load in GO data from B.imp

geneID2GO <- readMappings(file = "Bombus_impatiens_BP_All.txt", IDsep = ";", sep = "\t")

all working now - thank you!