as.newick: Convert a furcation tree into Newick format

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

Description

Convert a furcation tree into Newick format.

Usage

as.newick(furcation, allele = 0, side, hap.names = seq_len(furcation@nhap))

Arguments

furcation	an object of furcation-class.
allele	the allele to be considered (default 0).
side	side (either "left" or "right").
hap.names	names/labels of chromosomes in haplotype data file. Per default haplotypes are numbered by their order in the input file.

See Also

ftree-class, calc_furcation, plot.furcation

Examples

#example haplohh object (280 haplotypes, 1424 SNPs)
#see ?haplohh_cgu_bta12 for details
data(haplohh_cgu_bta12)
#calculate furcation for the marker "F1205400"
#which displays a strong signal of selection
f <- calc_furcation(haplohh_cgu_bta12, mrk = "F1205400")
#get left tree of ancestral allele (coded as '0')
as.newick(f, 0, "left")

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