Gabriel et al. (2002) haplotype blocks — morie

Pairs are strong-LD when the upper 95% profile-likelihood bound on D' exceeds 0.98 and the lower bound exceeds 0.7; strong recombination when the upper bound is below 0.9; blocks are maximal spans with >= 95% strong-LD informative pairs.

Usage

morie_hapblk(
  H,
  strong_hi = 0.98,
  strong_lo = 0.7,
  recomb_hi = 0.9,
  frac = 0.95
)

Arguments

H: Binary haplotype matrix (n x m).
strong_hi, strong_lo, recomb_hi: Paper thresholds.
frac: Required strong-LD fraction (0.95).

Value

A list with elements blocks (list of inclusive 0-based (start, end)), dprime, ci_lo, ci_hi, pair_class, method.

References

Gabriel, S. B. et al. (2002). The structure of haplotype blocks in the human genome. Science, 296(5576), 2225-2229.

Examples

V <- c(1, 2, 3, 4, 5, 6, 7, 8)
morie_hapblk(V)
#> $blocks
#> list()
#> 
#> $dprime
#>      [,1]
#> [1,]    0
#> 
#> $ci_lo
#>      [,1]
#> [1,]    0
#> 
#> $ci_hi
#>      [,1]
#> [1,]    0
#> 
#> $pair_class
#>      [,1]
#> [1,] ""  
#> 
#> $method
#> [1] "Gabriel et al. (2002) confidence-bound blocks"
#>