Skip to contents

Performing quick ORA analysis using Fisher or KS and an explicit background

Source: R/easytopGO.R
easytopGO.Rd

Runs topGO enrichment using an explicit eligible-gene universe. Fisher tests over-representation of selected genes; KS uses genuine gene-level p-value ranks for the complete background. Results can be plotted using easyGOPlot().

Usage

easytopGO(
  geneID,
  bkggset = NULL,
  gaf = "",
  useBiomart = TRUE,
  useGAF = FALSE,
  mart = "protists_mart",
  gset = "pfalciparum_eg_gene",
  algo = "weight01",
  stats = "fisher",
  category = "BP",
  fdr = FALSE,
  correction = "BY",
  cutoff = 0.05,
  go_cutoff = 0.05,
  return_GOdata = FALSE,
  OrgDb = NULL,
  orgdb_keytype = "GID"
)

Arguments

geneID

Uniquely named numeric vector of p-values in, named by gene ID. For Fisher, either selected genes or the complete tested vector may be supplied; genes with p-value < cutoff are selected. For KS, supply the actual p-value for EVERY gene in bkggset (not just DEGs).

bkggset

Nonempty character vector of all genes eligible for the analysis, typically genes eligible under your RNA-seq selection procedure. Required for both tests.

gaf

Path or URL to a GO Annotation File (GAF; .gz is supported). GAF column 2 must contain gene IDs corresponding to bkggset. When using this argument, set useBiomart=FALSE and useGAF=TRUE.

useBiomart

Logical To enable usage of BiomaRt to fetch GO terms. Default: TRUE.

useGAF

Logical To enable usage of custom .gaf file to fetch GO terms. Default: FALSE

mart, gset

BioMart name and dataset, respectively.

algo

Argument to specify which algorithm to be used for enrichment by topGO. For possible options use topGO::whichAlgorithms()

stats

Argument to specify the statistical test to be used for enrichment by topGO. For possible values use topGO::whichTests(). Default: "fisher".

category

Specify the category of Over-representation analysis such as "BP" for Biological Process, "MF" for Molecular Function and "CC" for Cellular Component Enrichment.

fdr

logical. Perform multiple testing correction testing. Default (FALSE)

correction

Adjustment method accepted by stats::p.adjust(). Possible values: ""holm", "hochberg", "hommel", "bonferroni", "BH", "BY","fdr". Read section 6.2 in topGO documentation before performing correction. Correction when using elim and weight is usually not recommended.

cutoff

P-value threshold defining selected genes, default 0.05. For KS this changes selected-gene reporting, not the KS statistic.

go_cutoff

Threshold for reporting raw GO p-values or adjusted GO p-values when fdr = TRUE.

return_GOdata

If TRUE, return the underlying topGOdata object.

OrgDb

An OrgDb object loaded by the caller, e.g. after running library(org.Pfalciparum3D7.eg.db). Passing it selects offline GO annotations instead of the default BioMart route.

orgdb_keytype

The key type of the IDs in bkggset and geneID. Default "GID" for custom packages built with AnnotationForge; check the keytypes available in your particular database.

Value

A data.frame with GO IDs, terms, numeric fisher or ks results, optional padj, and associated/selected genes. The gene_universe attribute gives available, feasible and selected-feasible counts. When return_GOdata = TRUE, returns a topGOdata object. Full descriptions of GO terms truncated by GenTable are restored when pRoloc is installed.

Details

The OrgDb route uses GO (direct annotations), leaving ancestor propagation to topGO. topGO itself depends on AnnotationDbi, so no additional installation or declared direct Import is needed for this route.

Examples

if (FALSE) { # \dontrun{
# res: DESeq2 results with Geneid, pvalue, padj and log2FoldChange.
ok <- !is.na(res$padj) & !is.na(res$Geneid)
background.gset <- res$Geneid[ok]
down <- ok & !is.na(res$log2FoldChange) &
  res$padj < 0.05 & res$log2FoldChange < 0
geneList <- stats::setNames(res$padj[down], res$Geneid[down])

# Fisher accepts a DEG-only list; the full universe is background.gset.
gores.fisher <- easytopGO(
  geneID = geneList, bkggset = background.gset,
  gaf = "annotation.gaf.gz", useBiomart = FALSE, useGAF = TRUE,
  stats = "fisher", category = "BP"
)

# Load your custom OrgDb package outside the function.
library(org.Pfalciparum3D7.eg.db)
pfdb <- org.Pfalciparum3D7.eg.db
gores.org <- easytopGO(
  geneID = geneList, bkggset = background.gset,
  OrgDb = pfdb, orgdb_keytype = "GID",
  stats = "fisher", category = "BP"
)
# KS
ok.ks <- ok & !is.na(res$padj)
bg.ks <- res$Geneid[ok.ks]
geneList.ks <- stats::setNames(res$padj[ok.ks], bg.ks)
gores.ks <- easytopGO(
  geneID = geneList.ks, bkggset = bg.ks,
  gaf = "annotation.gaf.gz", useBiomart = FALSE, useGAF = TRUE,
  stats = "ks", category = "BP"
)
} # }