calc_furcation: calculate furcation trees around a focal marker

In rehh: Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests

Description

Calculate furcation trees around a focal marker. A furcation tree captures in greater detail than EHH values the decrease of extended haplotype homozygosity at increasing distances from the selected focal marker.

Usage

calc_furcation(
  haplohh,
  mrk,
  allele = NA,
  limhaplo = 2,
  phased = TRUE,
  polarized = TRUE
)

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.
allele	a vector of alleles as coded internally, i.e. in case of polarized alleles, 0 represents the ancestral, 1 or higher the derived alleles. If NULL, all alleles of the focal marker are considered.
limhaplo	if there are less than limhaplo chromosomes that can be used for the calculation, it is stopped. This is useful in case of missing data, which lead to a successive exclusion of haplotypes: the further away from the focal marker the less haplotypes are evaluated.
phased	logical. If TRUE (default), chromosomes are expected to be phased. If FALSE, consecutive chromosomes are assumed to belong to diploid individuals and furcation trees are limited to within individuals which are homozygous at the focal marker.
polarized	logical. Affects only the order of furcations. If TRUE (default), the ancestral allele becomes the first furcation and derived alleles are sorted by their internal coding. Otherwise all alleles are sorted by their internal coding.

Details

A haplotype furcation tree visualizes the breakdown of LD at increasing distances from the focal marker. The root of each tree is an allele of the focal marker, which in turn is identified by a vertical dashed line. Moving either to the "left" or to the "right" of the focal marker, each further marker is an opportunity for a node; the tree either divides or does not, based on whether alleles at that marker distinguish between hitherto identical extended haplotypes. The thickness of the lines corresponds to the number of chromosomes sharing an extended haplotype.

Value

An object of class furcation, containing the furcation structure of the specified alleles at the focal marker.

References

Sabeti, P.C. and Reich, D.E. and Higgins, J.M. and Levine, H.Z.P and Richter, D.J. and Schaffner, S.F. and Gabriel, S.B. and Platko, J.V. and Patterson, N.J. and McDonald, G.J. and Ackerman, H.C. and Campbell, S.J. and Altshuler, D. and Cooper, R. and Kwiatkowski, D. and Ward, R. and Lander, E.S. (2002). Detecting recent positive selection in the human genome from haplotype structure. Nature, 419, 832-837.

See Also

plot.furcation, calc_haplen.

Examples

#example haplohh object (280 haplotypes, 1424 SNPs)
#see ?haplohh_cgu_bta12 for details
data(haplohh_cgu_bta12)
#plotting a furcation diagram for both ancestral and derived allele
#from the marker "F1205400"
#which display a strong signal of selection
f <- calc_furcation(haplohh_cgu_bta12, mrk = "F1205400")
plot(f)

rehh documentation built on Sept. 15, 2021, 5:06 p.m.