go_analaysis_gorilla: GO analysis with GOrilla

In JokingHero/ORFik: Open Reading Frames in Genomics

GO analysis with GOrilla

Description

Supports Gene symbols as default, and will produce the best results. You can also use ensembl gene ids, refseq gene ids and Entrez gene ids, but this will give weaker results.

Usage

go_analaysis_gorilla(
  target_genes,
  background_genes,
  organism,
  analysis_name = paste0("Go_analysis_", organism),
  open_browser = TRUE,
  pvalue_thresh = 0.01,
  db = "all"
)

Arguments

target_genes	a path to a txt file with the target Gene symbols, or presumed to be a character vector of genes (if length > 1). Minimum 10 genes, maximum 1 million.
background_genes	a path to a txt file with the background Gene symbols, or presumed to be a character vector of genes (if length > 1). Minimum 10 genes, maximum 2 million.
organism	organism(df), example "Homo sapiens"
analysis_name	character name, default "test". Used for saved file names and analysis name in GOrilla.
open_browser	= TRUE, open the URL
pvalue_thresh	fixed set numeric, default 0.001, Alternatives: 10e-3 to 10e-11
db	character, default "all". Which GO onthology categories to use, all means process, function and component. Alternatives: "proc", "func" and "comp", if you only want that single category subset.

Value

a url path to results, will also open your default web browser if open_browser is TRUE.

References

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-48

Examples

target_genes <- system.file("extdata/Homo_sapiens_sample/QC_STATS",
  "/DTEG_Comparison_Translation.txt", package = "ORFik")
background_genes <- system.file("extdata/Homo_sapiens_sample/QC_STATS",
  "/DTEG_Comparison_Background.txt", package = "ORFik")
#go_analaysis_gorilla(target_genes, background_genes, "Homo sapiens",
#                     analysis_name = "Translation vs background")

JokingHero/ORFik documentation built on June 9, 2025, 8:46 p.m.