inst/scripts/topgo_examples.r

In surh/HMVAR: Human Microbiome Variant Analysis in R

library(HMVAR)

dat <- read_eggnog("~/micropopgen/exp/2019/2019-04-01.hmp_subsite_annotations/annotations/Catonella_morbi_61904.emapper.annotations")
set.seed(123)
annots <- dat %>%
  dplyr::select(gene_id = query_name, terms = GO_terms)
annots
sig_genes <- annots$gene_id[1:200]

res <- test_go(genes = sig_genes, annots = annots)

topGO::GenTable(res$topgo_data, fisher = res$topgo_res)


annots <- dat %>%
  dplyr::select(gene_id = query_name, terms = GO_terms) %>%
  dplyr::bind_cols(score = rnorm(nrow(dat)))
annots
gsea(dat = annots, test = 'wilcoxon', alternative = 'greater', min_size = 10)