Annotate LD regions with genes

Overlaps a set of LD regions with a gene table and labels each region-gene pair with a `Gene_Relationship` (`GENE_CONTAINED`, `OVERLAPS_LEFT`, `OVERLAPS_RIGHT`, `CONTAINS_REGION`, or `OVERLAPS`). Region list columns (e.g. `GWAS_SNPs`) are preserved through the overlap. When `keep_intergenic = TRUE`, regions with no overlapping gene are retained as `INTERGENIC`.

Usage

hbr_annotate_regions_with_genes(
  regions,
  genes,
  chr_col = "Chromosome",
  start_col = "Region_Start",
  end_col = "Region_End",
  keep_intergenic = TRUE,
  verbose = TRUE
)

Arguments

regions

A `data.table` of LD regions.

genes

Gene table with ID, chromosome, start, end, and strand columns (column names auto-detected).

chr_col, start_col, end_col

Region coordinate column names.

keep_intergenic

Keep regions with no overlapping gene.

verbose

Print progress.

Value

A `data.table` of region-gene overlaps, or `NULL`.

Examples

regions <- data.table::data.table(
  LD_Region_ID = "R1",
  Chromosome   = "1",
  Region_Start = 1000L,
  Region_End   = 3000L)
genes <- data.table::data.table(
  Gene_ID         = "gene1",
  Gene_Chromosome = "1",
  Gene_Start      = 1000L,
  Gene_End        = 2500L,
  Gene_Strand     = "+")
hbr_annotate_regions_with_genes(regions, genes, verbose = FALSE)
#>    LD_Region_ID Chromosome Region_Start Region_End Gene_ID Gene_Name
#>          <char>     <char>        <int>      <int>  <char>    <char>
#> 1:           R1          1         1000       3000   gene1     gene1
#>    Gene_Function Gene_Chromosome Gene_Start Gene_End Gene_Strand
#>           <char>          <char>      <int>    <int>      <char>
#> 1:          <NA>               1       1000     2500           +
#>    Gene_Relationship Annotation_Status
#>               <char>            <char>
#> 1:    GENE_CONTAINED         Annotated