Pathway Enrichment Analysis

Perform hypergeometric test to identify enriched pathways among significant metabolite-mediated interactions

enrichPathways(
  object,
  pvalue_threshold = 0.05,
  min_overlap = 2,
  adjust_method = "BH"
)

Arguments

object

scMetaLink object with significant interactions

pvalue_threshold

Numeric. P-value cutoff for enrichment (default: 0.05)

min_overlap

Integer. Minimum overlap between significant metabolites and pathway (default: 2)

adjust_method

Character. P-value adjustment method (default: "BH")

Value

data.frame with enriched pathways and statistics

Examples

# \donttest{
# Perform pathway enrichment
enriched <- enrichPathways(result)
#> Error: object 'result' not found
head(enriched)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'head': object 'enriched' not found
# }