Saving the results of the topGO package as an R object (rda/rds file).
0
1
Entering edit mode
Ben ▴ 20
@ben-17772
Last seen 5 months ago
United States

Hi!

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) {
  methods::new(
    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 • 96 views
ADD COMMENT

Login before adding your answer.

Traffic: 579 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6