probhbd: Extracts the HBD probabilities from the zres object

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

Extracts the HBD probabilities from the zres object

Description

Extracts the locus specific HBD probabilities for an individual. A specific chromosomal region can be specified. A threshold T can be used to determine which HBD classes are used in the computation of the HBD probability. This function requires that the option "localhbd" was set to TRUE when creating the zres object.

Usage

probhbd(
  zres,
  zooin,
  id,
  chrom = NULL,
  startPos = NULL,
  endPos = NULL,
  T = FALSE
)

Arguments

zres	The name of the zres object created by the zoorun function.
zooin	The name of the zdata object created by the zoodata function. See "zoodata" for more details.
id	The number of the individual to extract.
chrom	the number of the chromosome where we are looking for HBD segments. This chromosome number refers to the position of the chromosome in the list of all chromsomes present in the input genotype data.
startPos	The starting position (on the chromosome) of the interval from which we will extract HBD segments (1 by default).
endPos	The ending position (on the chromosome) of the interval from which we will extract HBD segments (last position by default).
T	The value chosen to define the base population (to determine which classes are used in estimated of HBD probability, which classes are considered autozygous). When T is not provided, all HBD classes are considered to estimate the local HBD probability.

Value

The function returns a vector of HBD probabilities for the specified individual and chromosomal region. The HBD probabilities are computed as the sum of the probabilities for each HBD class with a rate smaller or equal than the threshold (the sum from all the HBD classes when T is not specified).

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