zoodoris: Returns number of HBD segments (or genome proportion) per...

In RZooRoH: Partitioning of Individual Autozygosity into Multiple Homozygous-by-Descent Classes

Returns number of HBD segments (or genome proportion) per size bins for DoRIS.

Description

The number of HBD segments in 1Mb bins is computed and the function returns a table that can be used with DoRIS to estimate paste effective population size. Alternatively, the proportion of the genome in the different 1 Mb bins is computed. The user must specify the range of the bins (the smallest and largest HBD segments considered). #'

Usage

zoodoris(zres, minv, maxv, glen, method = "counts")

Arguments

zres	The name of the zres object created by the zoorun function.
minv	The minimum length of HBD segments (in Mb) used for the DoRIS analysis.
maxv	The maximum length of HBD segments (in Mb) used for the DoRIS analysis.
glen	The length of the genome in Mb (including only the autosomes, the space where HBD segments have been searched for).
method	The argument is used to indicate that function will return counts of HBD segments (method = "counts") or proportion of the genome (method ="sharing") per 1 Mb bins.

Value

A data frame with three columns and one row per 1Mb bins. The first column indicates the the length of smallest HBD segments in the bin, the second column indicates the length of the largest HBD segments in the bin and the third column indicates the number of segments in the bin or the proportion of the genome in the bin.

RZooRoH documentation built on Oct. 27, 2023, 9:07 a.m.