# prepare environment
source(snakemake@params$setup_code_fname)
devtools::load_all("../..")
# run model
fit <- pareg::pareg(
study$df %>% select(gene, pvalue),
df_terms
)
df <- fit %>%
as.data.frame() %>%
mutate(method = "pareg_noterms", enrichment = abs(enrichment))
df %>%
arrange(desc(abs(enrichment))) %>%
head()
# misc
pareg_post_processing(fit, dirname(snakemake@output$fname))
# save result
df %>%
write_csv(snakemake@output$fname)
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