Saving the results of the topGO package as an R object (rda/rds file).
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Ben ▴ 50
Last seen 2.6 years ago
United States


I am trying to save the results object after executing the following command, which is explained in the topGO vignette:

go_analysis <- base::lapply(X = gene_universe, FUN = function(rrr) {
    Class = "topGOdata",
    description = "Test",
    ontology = "BP",
    allGenes = rrr,
    nodeSize = 10,
    annot = annFUN.gene2GO,
    gene2GO = goa_database_map

The go_analysis object in R has several elements (since executed using lapply) and is 348 MB in size according to the Global Environment window in RStudio.

Saving this object via save() or saveRDS() fails. By fails I mean R is working... and working... and working and the file size increases to over 1 GB without an end. I interrupt the session at some point because it does not make sense to me.

Any ideas? Same problems?

It should be a pretty straight forward process...

Thanks much.

RNASeq GO topGO Pathways • 677 views

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