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TinclG / PAS_analysis

Placenta Accreta Spectrum (PAS) disorders fall within the group of Placental Implantation Abnormalities. In this project we analysed differences in gene expression in the microenvironments of PAS and normal pregnancies.
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rbind of GOdata #10

Closed TinclG closed 2 years ago

TinclG commented 2 years ago

when creating GOdata objects, i tried to merge them with rbind (as in vignette):

1.0_analysis/3.0 topGO

Create topGOdata object

GOdataBP <- new("topGOdata", ontology = "BP", # use biological process ontology allGenes = geneList, geneSelectionFun = function(x)(x == 1), annot = annFUN.org, mapping = "org.Mm.eg.db", ID = "symbol") GOdataCC <- new("topGOdata", ontology = "CC", # use biological process ontology allGenes = geneList, geneSelectionFun = function(x)(x == 1), annot = annFUN.org, mapping = "org.Mm.eg.db", ID = "symbol") GOdataMF <- new("topGOdata", ontology = "MF", # use biological process ontology allGenes = geneList, geneSelectionFun = function(x)(x == 1), annot = annFUN.org, mapping = "org.Mm.eg.db", ID = "symbol") GOdata <- rbind(GOdataBP,GOdataCC,GOdataMF) _``` Error in rep(argl[[na]], length.out = nr) : attempt to replicate an object of type 'S4'

vjmarteau commented 2 years ago

I think you have human data right? mapping = "org.Mm.eg.db"