getIBDparameters: XIBD Parameter Estimation

In bahlolab/XIBD: Identity-by-Descent Analysis of the Human Genome

Description

Estimate the number of meioses and the probabilities of sharing 0, 1 and 2 alleles IBD between pairs.

Usage

getIBDparameters(ped.genotypes, number.cores = 1)

Arguments

ped.genotypes	a named list containing pedigree, genotypes and model. See Value description in getGenotypes for more details. The family IDs and individual IDs in pedigree must match the family IDs and individual IDs in the header of genotypes.
number.cores	the number of cores used for parallel execution.

Value

A named list containing autosome_parameters and X_chromosome_parameters. Both autosome_parameters and X_chromosome_parameters are data frames with columns:

1. Family 1 ID (type "character")

2. Individual 1 ID (type "character")

3. Family 2 ID (type "character")

4. Individual 2 ID (type "character")

5. The number of meiosis (type "numeric" or "integer")

6. Probability of sharing 0 alleles IBD (type "numeric")

7. Probability of sharing 1 allele IBD (type "numeric")

8. Probability of sharing 2 alleles IBD (type "numeric")

headed fid1, iid1, fid2, iid2, m, ibd0, ibd1 and ibd2, respectively. Each row describes parameters for a unique pair of samples. autosome_parameters will be NULL if chromosomes 1-22 are all excluded from ped.genotypes and X_chromosome_parameters will be NULL if chromosome 23 is excluded from ped.genotypes.

Examples

# estimate parameters
my_parameters <- getIBDparameters(ped.genotypes = example_genotypes,
                                  number.cores = 1)

str(my_parameters)

bahlolab/XIBD documentation built on May 11, 2019, 5:24 p.m.