# prepare environment
source(snakemake@params$setup_code_fname)
work_dir <- dirname(snakemake@output$fname)
gene_rank_fname <- file.path(work_dir, "genes.csv")
study$df %>%
select(gene, pvalue) %>%
write_csv(gene_rank_fname, col_names = FALSE)
term_fname <- file.path(work_dir, "terms.csv")
df_terms %>%
write_csv(term_fname, col_names = FALSE)
# run blitzGSEA
fname_out <- file.path(work_dir, "raw_result.csv")
system2("python", paste(
file.path(dirname(snakemake@input$script), "blitzgsea_code.py"),
gene_rank_fname,
term_fname,
fname_out
))
# format result
df <- read_csv(fname_out)
df %>%
head()
df %>%
rename(term = Term, enrichment = nes) %>%
select(term, enrichment) %>%
mutate(
method = "blitzgsea",
enrichment = abs(enrichment)
) %>%
write_csv(snakemake@output$fname)
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