ComputeFsegAllT: Computes inbreeding coefficients based on HBD segments...

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

Computes inbreeding coefficients based on HBD segments identified with the Viterbi algorithm (similar to a F_ROH estimator). Returns cumulative inbreeding coefficients estimated using different thresholds corresponding to the rates of the HBD classes.

Description

Computes inbreeding coefficients based on HBD segments identified with the Viterbi algorithm (similar to a F_ROH estimator). Returns cumulative inbreeding coefficients estimated using different thresholds corresponding to the rates of the HBD classes.

Usage

ComputeFsegAllT(zoores, zoodata, use_names = FALSE)

Arguments

zoores	a zoores object (output of zoorun)
zoodata	a zooin object (output of zoodata), it must be the zooin object associated to the zoores object
use_names	if TRUE, replaces numeric identifiers with the individual names (zoodata@sample_ids). In that case, zoodata@sample_ids must exit. Set to FALSE (default) for an IBD analysis (in that case ids do not correspond to sample_ids but to positions in the list of pairs).

Value

a data.frame with one row per individual and one column per HBD class (cumulative), column names being prefixed "F_class". The values are the inbreeding coefficient estimated using HBD segments associated with HBD classes with a rate lower or equal to the threshold.

RZooRoH documentation built on Oct. 3, 2026, 1:06 a.m.