getIBDsegments: IBD Segment Detection

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

Description

getIBDsegments() detects genomic regions shared IBD between all pairwise combinations of isolates.

Usage

getIBDsegments(ped.genotypes, parameters, number.cores = 1,
  minimum.snps = 20, minimum.length.bp = 50000, error = 0.001)

Arguments

ped.genotypes	A list containing 2 objects. See the Value description in getGenotypes for more details on this input.
parameters	A data frame containing meioses and IBD probability estimates for all pairwise combinations of isolates. See the Value description in getIBDparameters for more details on this input.
number.cores	Positive integer. The number of cores used for parallel execution.
minimum.snps	An integer value denoting the minimum number of SNPs in an IBD segment for it to be reported. The default value is 20 SNPs.
minimum.length.bp	The minimum length of a reported IBD segment. The default value is 50,000 bp.
error	The genotyping error rate. The default value is 0.001.

Value

A data frame with the following columns

1. Family 1 ID

2. Isolate 1 ID

3. Family 2 ID

4. Isolate 2 ID

5. Chromosome

6. Start SNP

7. End SNP

8. Start position bp

9. End position bp

10. Start position M

11. End position M

12. Number of SNPs

13. Length bp

14. Length M

15. IBD status (1 = one allele shared IBD, 2 = two alleles shared IBD)

where each row describes a unique IBD segment. The data frame is headed fid1, iid1, fid2, iid2, chr, start_snp, end_snp, start_position_bp, end_position_bp, start_position_M, end_position_M, number_snps, length_bp, length_M and ibd_status respectively.

See Also

getGenotypes and getIBDparameters.

Examples

## Not run: 
# prior to IBD detection, parameter estimates must be estimated.
# Assuming this has been done, IBD inference is performed
my_ibd <- getIBDsegments(ped.genotypes = png_genotypes,
                        parameters = png_parameters,
                        number.cores = 1,
                        minimum.snps = 20,
                        minimum.length.bp = 50000,
                        error = 0.001)

head(my_ibd)

## End(Not run)

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