predhbd: Extracts the IBD probabilities from the kres object

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

Extracts the IBD probabilities from the kres object

Description

Extracts the locus specific IBD probabilities for a pair of individuals. This is the probability that one pair of chromosomes (one sampled in each individual) are IBD at that position. A specific chromosomal region can be specified. A threshold T can be used to determine which classes are used in the computation of the IBD probability. This function requires that the option "localhbd" was set to TRUE when creating the kres object.

Usage

predhbd(
  kres,
  zooin,
  num,
  chrom = NULL,
  startPos = NULL,
  endPos = NULL,
  T = FALSE
)

Arguments

kres	The name of the kres object created by the zookin function.
zooin	The name of the zdata object created by the zoodata function. See "zoodata" for more details.
num	The number of the pair of individuals to extract (correspond to the position in the list of pairs).
chrom	the number of the chromosome where we are looking for IBD 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 IBD segments (1 by default).
endPos	The ending position (on the chromosome) of the interval from which we will extract IBD segments (last position by default).
T	The value chosen to define the base population (to determine which classes are used in estimated of IBD probability, which classes are considered autozygous). When T is not provided, all IBD classes are considered to estimate the local IBD probability.

Value

The function returns a vector of IBD probabilities averaged over the four combination of pairs of parental haplotypes for the specified pair of individuals and chromosomal region. The IBD probabilities are computed as the sum of the probabilities for each class with a rate smaller or equal than the threshold (the sum from all the IBD classes when T is not specified).

RZooRoH documentation built on June 8, 2025, 9:32 p.m.