Haplotype block table from a set of target loci

Runs [hbr_haplotype_blocks()] and returns the block summary table alongside the per-locus assignment. The table has one row per block with the block id, chromosome, start and end position in cM, the number of target loci in the block, the number of distinct genes (when `units` has a `gene` column) and the concatenated gene and trait names.

Usage

hbr_haplotype_block_table(
  plink_prefix = NULL,
  units,
  cm_snp = NULL,
  chr_snp = NULL,
  traits = NULL,
  method = c("recomb", "ld", "either", "fourgamete", "gabriel", "recomb+gabriel",
    "recomb+fourgamete"),
  flank_cM = 1,
  max_snps = 400L,
  max_span_cM = 5,
  min_gamete = 0.01,
  maf_min = 0.05,
  rmax = 0.01,
  r2 = 0.5,
  ld_max_cM = 3,
  r2_min = 0.25,
  gabriel_grid = 21L,
  carry = NULL
)

Arguments

plink_prefix

PLINK prefix, or an `hbr_run` object (in which case the run-level API is used). When the first positional argument is an `hbr_run`, this argument receives it.

units

Low-level API: data.frame with `chr` and `cm` per target locus, and `snp_col` when using the SNP-level methods. Alternatively, an `hbr_run` object (in which case the run-level API is used).

cm_snp, chr_snp

Low-level API: genetic positions and chromosomes of every SNP in the PLINK file.

traits

Optional character vector (one per row of `units`) of the trait(s) each locus belongs to. When `units` already carries a `traits` column, that is used instead.

method

One of the seven methods above.

flank_cM, max_snps, min_gamete

SNP-level methods only: window around the genes, SNPs kept per cluster, and gamete frequency that counts as recombination.

max_span_cM

Largest distance between the first and last locus of a block.

maf_min

Minimum minor-allele frequency.

rmax

Maximum Haldane recombination fraction between neighbours for `"recomb"`.

r2

Minimum carrier-indicator r-squared for `"ld"`.

ld_max_cM

Largest distance over which LD may join neighbours.

r2_min, gabriel_grid, carry

Reserved for future versions; kept for backward compatibility with the low-level API.

Value

A list with `blocks` (the summary table) and `assignment` (the block id per target locus, in the same order as `units`).

Examples

units <- data.frame(chr = c("1", "1", "1"),
                    cm  = c(10, 10.5, 11),
                    gene = c("g1", "g2", "g3"))
hbr_haplotype_block_table(method = "recomb", units = units)
#> $blocks
#>   block chr start_cM end_cM n_target_haplotypes n_genes    genes traits
#> 1 HB001   1       10     11                   3       3 g1;g2;g3     NA
#>   panel_freq
#> 1         NA
#> 
#> $assignment
#> [1] 1 1 1
#>