Export GO term names as TERM2NAME

Returns a two-column data.frame suitable for clusterProfiler::enricher(TERM2NAME = ...).

The returned table is restricted to GO terms present in the current GO or GOSubgraph object.

Optional size filtering can be applied based on the number of mapped genes per GO term.

Usage

as_term2name(go, minGSSize = NULL, maxGSSize = NULL)

Arguments

go

A GO or GOSubgraph object.

minGSSize

Minimum number of genes per GO term.

maxGSSize

Maximum number of genes per GO term.

Value

A data.frame with columns term and name.

Examples

data("go_cc_ecoli", package = "GOcontext")

# Export GO term names for the current graph
term2name <- as_term2name(go_cc_ecoli)
head(term2name)
#>         term                                        name
#> 1 GO:0000015           phosphopyruvate hydratase complex
#> 2 GO:0000109          nucleotide-excision repair complex
#> 3 GO:0000110 nucleotide-excision repair factor 1 complex
#> 4 GO:0000111 nucleotide-excision repair factor 2 complex
#> 5 GO:0000112 nucleotide-excision repair factor 3 complex
#> 6 GO:0000113 nucleotide-excision repair factor 4 complex

# Apply size filtering based on mapped genes
term2name_filtered <- as_term2name(
    go = go_cc_ecoli,
    minGSSize = 5,
    maxGSSize = 100
)
head(term2name_filtered)
#>         term                                          name
#> 1 GO:0000345 cytosolic DNA-directed RNA polymerase complex
#> 2 GO:0000428           DNA-directed RNA polymerase complex
#> 3 GO:0000935                               division septum
#> 4 GO:0005576                          extracellular region
#> 5 GO:0005667               transcription regulator complex
#> 6 GO:0005694                                    chromosome