Over-Representation Analysis Using enrichGO — ora

Performs Gene Ontology (GO) over-representation analysis (ORA) using enrichGO on differential expression results. Genes can be analyzed separately based on their direction of differential expression (upregulated or downregulated).

Usage

ora_enrichgo(
  filtered_results,
  direction = c("up", "down"),
  log2fc_thresh = 1,
  pval_thresh = 0.05,
  top_terms = 15,
  OrgDb = org.Hs.eg.db,
  keyType = "ENSEMBL",
  ont = "BP"
)

Arguments

filtered_results: list of tables or a table of differential expression results
direction: Which direction +log2fc -log2fc should be looked at ? e.g. "up", "down"
log2fc_thresh: what is log2FC cutoff you would want for the analysis
pval_thresh: after running fisher exact test for ORA, what should the distribution of pvalues be?
top_terms: How many resulting terms should be display in the visuals.
OrgDb: rganism database. Default is human: org.Hs.eg.db. Other organism annotation databases are available from https://bioconductor.org/packages/3.23/data/annotation/.
keyType: which type of geneid are being entered into the cluster
ont: which ontological DB will you be using ? options c("BP", "CC", "MF")

Value

A list containing:

enrichgo_results: Results from the GO over-representation analysis returned by enrichGO.
visuals: A collection of visualizations summarizing the enriched GO terms, including dotplots and barplots.

Details

Genes are first separated according to their direction of differential expression and filtered using the supplied log2 fold-change and p-value thresholds. Over-representation analysis is then performed using enrichGO.

Examples

if (FALSE) { # \dontrun{
    enrich_ora_results <- ora_enrichgo(filtered_results,
                                 direction = c("up", "down"),
                                     log2fc_thresh = 1,
                                      pval_thresh = 0.05,
                                      top_terms = 15,
                                      OrgDb = org.Hs.eg.db,
                                     keyType = "ENSEMBL",
                                       ont = "BP")
} # }