In LUMC/dgeAnalysis: dgeAnalysis

Load packages

## Load required packages
suppressPackageStartupMessages({
  library(gprofiler2)
})

Input

Load input variables

## Import variables
geneList <- strsplit(params$geneList, "\n")[[1]]
organism <- params$organism
significant <- eval(parse(text = params$significant))
alfa <- params$alfa
database <- params$database

Show input variables

## Values of variables
length(geneList)
organism
significant
alfa
database

Run enrichment

## Start enrichment with gProfiler
enrich <- gost(
  query = geneList,
  organism = organism,
  ordered_query = FALSE,
  significant = significant,
  user_threshold = alfa,
  correction_method = "gSCS",
  domain_scope = "annotated",
  sources = database,
  evcodes = TRUE
)

Show results

## Show results
enrich$result$query <- ""
gostplot(enrich, capped = FALSE, interactive = FALSE)

Save results

## Save data files
save(enrich, file = "enrichment.RData")

Session info

## Session info
sessionInfo()

LUMC/dgeAnalysis documentation built on Aug. 16, 2022, 6:23 a.m.