getIBDparameters: Parameter Estimation

In bahlolab/isoRelate: Identity-by-Descent Inference of Haploid Recombining Organisms

Description

getIBDparameters() estimates the number of meiosis and the probabilities of sharing 0, 1 and 2 alleles IBD between all pairwise combinations of isolates.

Usage

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

Arguments

ped.genotypes	A list containing 2 objects. See the Value description in getGenotypes for more details on this input. Note the family IDs and isolate IDs in object 1 of this list must match the family IDs and isolate IDs in the header of object 2 of this list.
number.cores	Positive integer. The number of cores used for parallel execution.

Value

A data frame with the following eight columns:

1. Family 1 ID

2. Isolate 1 ID

3. Family 2 ID

4. Isolate 2 ID

5. The number of meiosis separating the pair

6. Probability of sharing 0 alleles IBD

7. Probability of sharing 1 allele IBD

8. Probability of sharing 2 alleles IBD

where each row describes a unique pair of isolates. The data frame is headed fid1, iid1, fid2, iid2, m, ibd0, ibd1 and ibd2 respectively.

See Also

getGenotypes and getIBDsegments.

Examples

# following processing and filtering of genotype data,
# we estimate the proportion of genome shared IBD
my_parameters <- getIBDparameters(ped.genotypes = png_genotypes,
                                  number.cores = 1)

head(my_parameters)

bahlolab/isoRelate documentation built on May 11, 2019, 5:25 p.m.