Runs of homozygosity: F_ROH per animal and per-marker frequency

Runs of homozygosity: F_ROH per animal and per-marker frequency

Usage

roh(m, min_snp = 30L, max_het = 0L, pos = NULL, min_kb = NULL, chr = NULL)

Arguments

m

0/1/2 matrix; NA breaks the run, it is never treated as homozygous. Double, integer and raw storage give the same result; in a raw matrix 5 is the missing code

min_snp

minimum run length, in consecutive markers

max_het

heterozygotes tolerated inside a run (0 = none)

pos

positions in base pairs, optional; with them min_kb also filters

min_kb

minimum length in kb, used only when pos is given

chr

chromosome of each marker, optional; runs do not cross chromosomes

Without a map, the run is defined by the COUNT of consecutive markers, and the limitation is stated: panels of different density give different runs with the same min_snp.

Value

list with animal (F_ROH = fraction of the markers in ROH) and marker (frequency of animals in ROH at each marker: the peaks are the islands)

References

McQuillan, R. et al. (2008). Runs of homozygosity in European populations. American Journal of Human Genetics 83:359-372.