get.roh: Runs of homozygosity

In cgmisc-team/cgmisc: Various functions useful in computational genetics, e.g. in GWAS

Runs of homozygosity

Description

Identifies runs of homozygosity in overlapping windows across chromosome.

Usage

get.roh(data, chr, LW, hetero.zyg, threshold = 0.23, strict = TRUE)

Arguments

data	a gwaa.data class object as used by gwaa.data-class
chr	number of chromosome
LW	a matrix of windows coordinares returned by get.overlap.windows function
hetero.zyg	a matrix of average heterozygosities for windows returned by het.overlap.wind function
threshold	threshold of homozygosity. All windows with homozygosity below this limit will be treated as homozygous.
strict	if one window with lower homozygosity should be tolerated

Value

matrix with columns respectively : 1) number of first window of run, 2) coordinate of first window in a run, 3) coordinate of last window in a run, 4) length of run (number of windows)

Author(s)

Marcin Kierczak <[e-mail]>, Jagoda Jablonska <[e-mail]>

See Also

get.overlap.windows het.overlap.wind

cgmisc-team/cgmisc documentation built on Jan. 3, 2024, 9:52 p.m.