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Run gene ontology enrichment with elimination method.

gse_go_elim_method.Rd

This method takes the GeneOntologyElim and a target gene set and performs an GSE enrichment leveraging ontological information. It starts at the lowest levels of the ontology and tests if there is significant enrichment for any GO terms. If the threshold of the p-value is below the elimination threshold, the genes from this term will be removed from all its ancestors. The function then proceeds to the next level of the ontology and repeats the process. The gene universe will be automatically set to every gene represented in the ontology.

Usage

gse_go_elim_method(
  object,
  target_genes,
  minimum_overlap = 3L,
  fdr_threshold = 0.05,
  elim_threshold = 0.05,
  min_genes = NULL
)

Arguments

object

The underlying class, see GeneOntologyElim().

target_genes

String. The target genes you wish to apply the GSEA over.

minimum_overlap

Integer. Threshold for the minimal overlap.

fdr_threshold

Float. Threshold for maximum fdr to include in the output.

elim_threshold

Float. Threshold from which p-value onwards the elimination on the ancestors shall be conducted.

min_genes

Integer. Minimum number of genes that have to be included in the gene ontology term. If NULL, it will default to the number of minimum genes stored in GeneOntologyElim.

Value

data.table with enrichment results.

Examples

# \donttest{
# human GO terms with at least 25 genes
go_obj <- GeneOntologyElim(
  get_go_data_human(.verbose = FALSE),
  min_genes = 25L
)
target_genes <- unique(unlist(S7::prop(go_obj, "go_to_genes")[1:5]))
head(gse_go_elim_method(go_obj, target_genes = target_genes), 3)
#>         go_id                                  go_name odds_ratios
#>        <char>                                   <char>       <num>
#> 1: GO:0007411                            axon guidance         Inf
#> 2: GO:0000244  spliceosomal tri-snRNP complex assembly         Inf
#> 3: GO:0000353 formation of quadruple SL/U4/U5/U6 snRNP         Inf
#>            pvals           fdr  hits gene_set_lengths
#>            <num>         <num> <num>            <num>
#> 1:  0.000000e+00  0.000000e+00   192              192
#> 2: 2.939673e-140 2.850013e-137    76               76
#> 3: 1.335653e-104 8.632771e-102    57               57
# }