Description Usage Arguments Value
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.
1 | IBDTable(ibd.results)
|
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. |
A data frame containing a summary of all IBD segments inferred for this pair of isolates. The data frame contains the following columns:
Family 1 ID
Isolate 1 ID
Family 2 ID
Isolate 2 ID
Chromosome
SNP identifier
Start SNP
End SNP
Start position bp
End position bp
Start position M
End position M
Number of SNPs
Length bp
Length M
IBD status (1 = 1 allele shared IBD, 2 = 2 alleles shared IBD)
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