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Run MSigDB enrichment directly from a VISTA comparison

get_msigdb_enrichment.Rd

Convenience wrapper that pulls regulated genes from a stored differential expression comparison in a VISTA object and runs enrichMsigDB() on them.

Usage

get_msigdb_enrichment(
  x,
  sample_comparison,
  regulation = c("Up", "Down", "Both", "All"),
  from_type = "SYMBOL",
  orgdb,
  msigdb_category = "H",
  msigdb_subcategory = NULL,
  species = "Mus musculus",
  background = NULL,
  col_genetype = "GENETYPE",
  feature_type = "protein-coding",
  ...
)

Arguments

x

A VISTA object with DE results in metadata(x)$de_results.

sample_comparison

Character scalar naming the comparison to use.

regulation

One of "Up", "Down", "Both", or "All"; selects which genes to send to enrichment.

from_type

Identifier type of the genes in the DE table (passed to enrichMsigDB(), default "SYMBOL"). Ensembl versions are stripped automatically.

orgdb

An OrgDb object used for ID conversion (passed through). If omitted, the default is chosen from species (mouse/human).

msigdb_category

MSigDB category (e.g., "H", "C2", "C5"). Default "H".

msigdb_subcategory

Optional MSigDB sub-collection. Default NULL.

species

Species name for MSigDB (default "Mus musculus").

background

Optional background gene set (passed to enrichMsigDB()). Default NULL uses all features in x (optionally filtered by feature_type).

col_genetype

Column in rowData(x) used to filter background by gene type. Default "GENETYPE".

feature_type

Gene type to retain in the background when filtering. Default "protein-coding".

...

Additional arguments forwarded to enrichMsigDB().

Value

A list with enrich containing an enrichResult.

Examples

if (requireNamespace("msigdbr", quietly = TRUE)) {
  vista <- example_vista()
  comp <- names(comparisons(vista))[1]
  msig <- get_msigdb_enrichment(
    vista,
    sample_comparison = comp,
    regulation = "Both",
    msigdb_category = "H",
    from_type = "ENSEMBL"
  )
  class(msig$enrich)
}
#> [1] "enrichResult"
#> attr(,"package")
#> [1] "DOSE"

# \donttest{
# Create VISTA object
data("count_data", package = "VISTA")
data("sample_metadata", package = "VISTA")

vista <- create_vista(
  counts = count_data[1:200, ],
  sample_info = sample_metadata[1:6, ],
  column_geneid = "gene_id",
  group_column = "cond_long",
  group_numerator = "treatment1",
  group_denominator = "control"
)
#> estimating size factors
#> estimating dispersions
#> gene-wise dispersion estimates
#> mean-dispersion relationship
#> final dispersion estimates
#> fitting model and testing
comp <- names(comparisons(vista))[1]

# Run MSigDB enrichment on upregulated genes
msig_up <- get_msigdb_enrichment(
  vista,
  sample_comparison = comp,
  regulation = "Up",
  msigdb_category = "H",  # Hallmark gene sets
  from_type = "ENSEMBL"
)

if (!is.null(msig_up$enrich)) {
  # View results
  head(msig_up$enrich)
  # Visualize enrichment
  get_enrichment_plot(msig_up$enrich)
}


# Enrichment for downregulated genes
msig_down <- get_msigdb_enrichment(
  vista,
  sample_comparison = comp,
  regulation = "Down",
  msigdb_category = "C2"  # Curated gene sets
)
# }