Entering edit mode
I'd like to use the GOsummaries package in a workflow that I'm building. But I do not understand the rationale behind how the genes1 and genes2 vectors were constructed in the package vignette (page 2): https://bioconductor.org/packages/release/bioc/vignettes/GOsummaries/inst/doc/GOsummaries-basics.pdf. I have a gene list like mygenes = c("some_gene1", "some_gene2", ... "some_geneN") that I'd like to use the GOsummaries package with. Do I need to assign my gene list to one object (e.g., genes1) and then assign the entire genome gene list to another object (e.g., genes2) and then do gl = list(List = list(genes1, genes2)) or is there some other way?
This is the error I now get:
P.S. Doesn't one need to also specify the organism prior to generating a word cloud (i.e., for the apriori GO enrichment analysis)? Here, my gene list has an RGD entry, so is clearly rat, but how would the GOsummaries package know what organism you're working with ahead of time? Thanks for clarifying.