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A function to reduce go terms by semantic similarity

Source: R/bb_gosummary.R
bb_gosummary.Rd

A function to reduce go terms by semantic similarity

Usage

bb_gosummary(
  x,
  reduce_threshold = 0.8,
  go_db = c("org.Hs.eg.db", "org.Dr.eg.db", "org.Mm.eg.db")
)

Arguments

x

A list go term enrichment results produced by bb_goenrichment.

reduce_threshold

The degree of term reduction. 0 to 1. Higher is more reduction.

go_db

The database to query. Choose from c("org.Hs.eg.db", "org.Dr.eg.db", "org.Mm.eg.db", ...).

Value

A list with three items:

simMatrix

The GO term semantic similarity matrix from calculateSimMatrix.

scores

A named numeric vector, one entry per GO term in x$res_table, giving -log10(classicFisher) for that term's enrichment p-value (from x$res_table$classicFisher). Higher values indicate stronger enrichment.

reducedTerms

The term-reduction result from reduceSimMatrix, whose score column is this same -log10(classicFisher) value for each retained term.