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Enumerate IBD partitions consistent with a given relationship graph

Source: R/enumerate_IPs_RG.R
enumerate_IPs_RG.Rd

Enumerate IBD partitions consistent with a given relationship graph; see vignette("enumerate") for more details.

Usage

enumerate_IPs_RG(RG, compat = TRUE)

Arguments

RG

A relationship graph; see enumerate_RGs for details.

compat

Logical, if true, a list of partitions equivalence objects are returned. Otherwise, returns a list of IBD partition vectors in reference to the sibling clusters.

Details

For a IBD partition to be consistent with the relationship graph given, it must satisfy the following:

  • genotypes within each IBD cell have clonal and sibling relationships only,

  • genotypes that are clones must be in the same IBD cell,

  • each cluster of sibling units span at most 2 IBD cells (corresponds to two parents).

Note that all IBD partitions are equally likely.

Examples

set.seed(3)
RG <- sample_RG(c(2, 1, 2))
enumerate_IPs_RG(RG)
#> [[1]]
#> [1] {g1,g4,g5}{g2,g3}
#> 
#> [[2]]
#> [1] {g1}{g4,g5}{g2,g3}
#> 
#> [[3]]
#> [1] {g1,g4}{g5}{g2,g3}
#> 
#> [[4]]
#> [1] {g1,g5}{g4}{g2,g3}
#> 
#> [[5]]
#> [1] {g1,g4,g5}{g2}{g3}
#> 
#> [[6]]
#> [1] {g1}{g4,g5}{g2}{g3}
#> 
#> [[7]]
#> [1] {g1,g4}{g5}{g2}{g3}
#> 
#> [[8]]
#> [1] {g1,g5}{g4}{g2}{g3}
#>