Define Gene-Based Genomic Regions

Source: R/define_regions.R

Creates a standard region table from a gene boundary table. Each gene becomes one region for variant-set analysis.

define_regions_gene(genes_info = NULL, chr = NULL, extend = 0L)

Arguments

genes_info

Data frame with gene boundaries. Default NULL uses the bundled STAARpipeline genes_info (18,445 protein-coding genes). Accepts STAARpipeline format (hgnc_symbol, chromosome_name, start_position, end_position) or simplified format (gene, chr, start, end).

chr

Integer or character chromosome(s) to include. NULL for all.

extend

Integer bp to extend gene boundaries on each side. Default 0.

Value

Data frame with columns: region_id, chr, start, end, label.

Examples

# With a user-provided gene table
my_genes <- data.frame(
  gene = c("BRCA1", "TP53"),
  chr = c("17", "17"),
  start = c(43044295L, 7668402L),
  end = c(43125364L, 7687550L)
)
regions <- define_regions_gene(my_genes)
regions
#>   region_id chr    start      end label
#> 1     BRCA1  17 43044295 43125364 BRCA1
#> 2      TP53  17  7668402  7687550  TP53

# Extend boundaries by 1kb on each side
regions_ext <- define_regions_gene(my_genes, extend = 1000)