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Go Term Enrichment

Source: R/bb_goenrichment.R
bb_goenrichment.Rd

A function to find enriched go terms from a query list of gene names relative to a reference list of gene names.

Usage

bb_goenrichment(
  query,
  reference,
  group_pval = 0.01,
  go_db = c("org.Hs.eg.db", "org.Dr.eg.db", "org.Mm.eg.db")
)

Arguments

query

A vector of gene names

reference

The background gene list. Usually will be as_tibble(rowData(cds_main)).

group_pval

P value to determine enrichment. Default: 0.01.

go_db

GO term database Default: c("org.Hs.eg.db", "org.Dr.eg.db", "org.Mm.eg.db")

Value

A list with three items:

sampleGOdata

The topGOdata object built from query/reference.

resultFisher

The topGOresult object returned by runTest().

res_table

A tibble of the top 100 GO terms (by GenTable), with classicFisher replaced by the raw numeric p-values taken directly from resultFisher@score (rather than GenTable's character-formatted, precision-truncated values) so downstream consumers (e.g. bb_gosummary) receive a numeric column.