Extract genes from enriched pathways

Parses pathway-level gene members from an enrichment result and returns either a long table, pathway-indexed list, or a unique vector of genes.

Usage

get_pathway_genes(
  x,
  pathways = NULL,
  top_n = 10,
  pathway_column = c("Description", "ID"),
  gene_column = c("auto", "geneID", "core_enrichment"),
  gene_sep = "/",
  return_type = c("long", "list", "vector")
)

Arguments

x

An enrichResult/gseaResult, or a list containing element enrich (e.g. output from get_msigdb_enrichment()).

pathways

Optional character vector of pathway names to keep. Matches against pathway_column.

top_n

Number of top pathways to use when pathways is NULL. Ranking uses p.adjust (then pvalue) when available. Default: 10.

pathway_column

Which enrichment column to match pathway names against: "Description" (default) or "ID".

gene_column

Which column stores pathway members. "auto" (default) uses "geneID" when present, otherwise "core_enrichment".

gene_sep

Delimiter used in pathway gene strings (default "/").

return_type

One of "long", "list", or "vector".

Value

Depending on return_type:

• "long": data frame with pathway_id, pathway, and gene.

• "list": named list of character vectors (genes per pathway).

• "vector": unique character vector of genes.

Examples

if (FALSE) { # \dontrun{
data("count_data", package = "VISTA")
data("sample_metadata", package = "VISTA")

vista <- create_vista(
  counts = count_data,
  sample_info = sample_metadata,
  column_geneid = "gene_id",
  group_column = "cond_long",
  group_numerator = "treatment1",
  group_denominator = "control"
)

msig <- get_msigdb_enrichment(
  vista,
  sample_comparison = names(comparisons(vista))[1],
  regulation = "Up",
  species = "Homo sapiens",
  from_type = "ENSEMBL"
)

pathway_tbl <- get_pathway_genes(msig, top_n = 5, return_type = "long")
head(pathway_tbl)
} # }