calc_pairwise_haplen: Calculate pairwise shared haplotype length between all chromosomes

Description

Calculate pairwise shared haplotype length between all chromosomes at a focal marker.

Usage

calc_pairwise_haplen(
  haplohh,
  mrk,
  phased = TRUE,
  maxgap = NA,
  max_extend = NA,
  side = "both"
)

Value

The returned value is a matrix with pairwise shared haplotype lengths.

Arguments

haplohh: an object of class haplohh (see data2haplohh).
mrk: integer representing the number of the focal marker within the haplohh object or string representing its ID/name.
phased: logical. If TRUE (default) chromosomes are expected to be phased. If FALSE, the haplotype data is assumed to consist of pairwise ordered chromosomes belonging to diploid individuals and only the two chromosomes of each individual are compared.
maxgap: maximum allowed gap in bp between two markers. If exceeded, further calculation is stopped at the gap (default=NA, i.e. no limitation).
max_extend: maximum distance in bp to extend shared haplotypes away from the focal marker. (default NA, i.e. no limitation).
side: side to consider, either "left" (positions lower than focal position), "right" (positions higher than focal position) or "both" (default).

Details

The function computes the length of shared haplotypes (stretches of identical sequence) around the focal marker.

Note that the function calc_haplen calculates for each chromosome the boundaries of its longest shared haplotype; separately upstream and downstream of the focal marker.

Examples

Run this code

#example haplohh object (280 haplotypes, 1424 SNPs)
#see ?haplohh_cgu_bta12 for details
data(haplohh_cgu_bta12)
#computing shared haplotype lengths around the marker "F1205400"
#which displays a strong signal of selection
m <- calc_pairwise_haplen(haplohh_cgu_bta12, mrk = "F1205400")
#note that calc_haplen() returns the length of the longest shared haplotype:
f <- calc_furcation(haplohh_cgu_bta12, mrk = "F1205400")
h <- calc_haplen(f)
#all pairwise shared haplotype lengths to the left of the focal marker
m_left <- calc_pairwise_haplen(haplohh_cgu_bta12, mrk = "F1205400", side = "left")
#get for each chromosome the maximum shared haplotype length
max_left <- apply(m_left, 1, max)
all.equal(max_left, h$position - h$haplen$MIN, check.attributes = FALSE)
#the same for shared haplotypes to the right of the focal marker
m_right <- calc_pairwise_haplen(haplohh_cgu_bta12, mrk = "F1205400", side = "right")
max_right <- apply(m_right, 1, max)
all.equal(max_right, h$haplen$MAX - h$position, check.attributes = FALSE)