Entering edit mode
Hi,
I'm using ReactomePA and I want to create a list of all reactome pathway of the GO term analysis.
gsepa <- gsePathway(geneList,
organism = "mouse",
exponent = 1,
minGSSize = 10,
maxGSSize = 500,
pvalueCutoff = "none",
pAdjustMethod = "BH",
verbose = TRUE,
seed = FALSE)
go.df <- data.frame(gsepa)
go.df <- lsr::sortFrame(go.df, pvalue)
GOList <- vector('list', nrow(go.output))
for (i in 1:length(go.df$Description)) {
GOList[[i]] <- viewPathway(go.df$Description[[i]],
readable = TRUE,
organism = "mouse",
foldChange = geneList)
}
I get following error
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘convertIdentifiers’ for signature ‘"NULL"’
Any ideas how to solve this? When I run the viewPathway
function individually the plots appear, so I assume it's something with my loop.
Thanks!