IBDTable: Internal Function

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

Description

IBDTable() produces summaries of detected IBD segments for a single pair of isolates. These summaries include the genetic map start and end of IBD segments in bp, cM and SNP identifiers; and lengths of IBD segments in bp, cM and SNPs.

Usage

IBDTable(ibd.results)

Arguments

ibd.results

A data frame containing family ID and isolate ID for isolate 1, family ID and isolate ID for isolate 2, numeric SNP identifiers, chromosome identifiers, genetic map positions of SNPs in Morgans (M) and base-pairs (bp) and the Viterbi results respectively, for all SNPs.

Value

A data frame containing a summary of all IBD segments inferred for this pair of isolates. The data frame contains the following columns:

1. Family 1 ID

2. Isolate 1 ID

3. Family 2 ID

4. Isolate 2 ID

5. Chromosome

6. SNP identifier

7. Start SNP

8. End SNP

9. Start position bp

10. End position bp

11. Start position M

12. End position M

13. Number of SNPs

14. Length bp

15. Length M

16. IBD status (1 = 1 allele shared IBD, 2 = 2 alleles shared IBD)

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