Get Genes by Regulation — get_genes_by

Extract gene IDs by regulation class from selected comparisons in a VISTA object.

Usage

get_genes_by_regulation(
  x,
  sample_comparisons,
  regulation = "Both",
  top_n = NULL,
  display_id = NULL,
  return_type = c("list", "table")
)

Arguments

x: A VISTA object.
sample_comparisons: Character vector of comparison names to include.
regulation: One of "Up", "Down", "Both", or "All" (default: "Both").
top_n: Optional integer limiting each comparison to the top DE genes ranked by absolute log2 fold change after regulation filtering.
display_id: Optional column name in rowData(x) to append when return_type = "table", for example "SYMBOL".
return_type: Either "list" (default) to return gene ID vectors or "table" to return one data frame per comparison with gene metadata.

Value

A named list of character vectors (one per comparison) when return_type = "list", or a named list of data frames when return_type = "table".

Examples

v <- example_vista()
comp <- names(comparisons(v))[1]
genes <- get_genes_by_regulation(v, sample_comparisons = comp, regulation = 'Up', top_n = 20)
str(genes, max.level = 1)
#> List of 1
#>  $ treatment1_VS_control: chr [1:2] "ENSG00000004799" "ENSG00000003402"