rohbd: Extracts the HBD segments from the zres object

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

Extracts the HBD segments from the zres object

Description

Extracts the HBD segments (or RoH) from the zres object. Extraction is performed for the indicated individuals and the selected region (all by default).

Usage

rohbd(
  zres,
  ids = NULL,
  chrom = NULL,
  startPos = NULL,
  endPos = NULL,
  inside = TRUE
)

Arguments

zres	The name of the zres object created by the zoorun function.
ids	An array with the ids of the individuals to extract. All individuals are extracted by default.
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).
inside	A logical indicating whether we extract only segment within the interval (TRUE) or overlapping with the interval (FALSE). By 'within the interval', we mean that both starting and end position of the HBD segment should be in the interval. By 'overlapping', we mean that at least one part of the HBD segment should be located in the interval.

Value

The function returns a data frame with the HBD segments fitting the filtering rules (id and position). The data frame has one line per identified HBD segment and nine columns: id is the number of the individual in which the HBD segments is located, chrom is the chromosome of the HBD segments, start_snp is the number of the SNP at which the HBD segment starts (the SNP number within the chromosome), start_end is the number of the SNP at which the HBD segment ends (the SNP number within the chromosome), start_pos is the position at which the HBD segment starts (within the chromosome), start_end is the position at which the HBD segment ends (within the chromosome), number_snp is the number of consecutive SNPs in the HBD segment, length is the length of the HBD segment (for instance in bp or in cM/1000000) and HBDclass is the HBD class associated with the HBD segment.

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