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Generate gene genealogy from samples

Source: R/genealogy.R
genealogy.Rd

An individual-based family tree stored in sample_family is transformed into a gene-based table with gather_segments(). Then, the ancestry of each gene/segment is randomly assigned in make_gene_genealogy(). Sampled segments and their ancestors can be annotated with annotate_sampled().

Usage

make_gene_genealogy(samples)

gather_segments(samples)

count_uncoalesced(genealogy)

annotate_sampled(genealogy)

Arguments

samples

A data.frame: sample_family or its tranfromation by gather_segments(). Using the latter will improve performance when the function is called many times, e.g., in make_snp().

genealogy

An output from make_gene_genealogy().

Value

An igraphlite object with genealogy subclass.

gather_segments() transforms an individual-based sample_family into a segment-based table.

count_uncoalesced() returns the count of uncoalesced roots of the genealogy.

annotate_sampled() adds the "sampled" edge attribute to the genealogy: TRUE if sampled, FALSE if upstream of samples, NA if unrelated.

See also

make_snp() for SNP generation using genealogy.

Examples

set.seed(666)
result = tekka("-y20 -l2 --sa 2,2 --sj 2,2")
samples = result$sample_family[[1L]]
segments = gather_segments(samples)
segments
#> # A tibble: 152 × 4
#>    id    birth_year capture_year parent_id
#>    <chr>      <int>        <int>     <int>
#>  1 7-1           20           20        55
#>  2 7-2           20           20        53
#>  3 8-1           20           20        58
#>  4 8-2           20           20        56
#>  5 15-1          20           20        73
#>  6 15-2          20           20        72
#>  7 16-1          20           20        14
#>  8 16-2          20           20        75
#>  9 3-1           19           19        38
#> 10 3-2           19           19        13
#> # ℹ 142 more rows

genealogy = make_gene_genealogy(segments)
genealogy
#> $V  tibble [154 × 1] (S3: tbl_df/tbl/data.frame)
#>  $ name: chr [1:154] "55-1" "7-1" "53-1" "7-2" ...
#> # A tibble: 152 × 4
#>    from  to    birth_year capture_year
#>    <chr> <chr>      <int>        <int>
#>  1 55-1  7-1           20           20
#>  2 53-1  7-2           20           20
#>  3 58-2  8-1           20           20
#>  4 56-2  8-2           20           20
#>  5 73-1  15-1          20           20
#>  6 72-1  15-2          20           20
#>  7 14-2  16-1          20           20
#>  8 75-1  16-2          20           20
#>  9 38-2  3-1           19           19
#> 10 13-1  3-2           19           19
#> # ℹ 142 more rows

count_uncoalesced(genealogy)
#> [1] 12

annotate_sampled(genealogy)
#> $V  tibble [154 × 1] (S3: tbl_df/tbl/data.frame)
#>  $ name: chr [1:154] "55-1" "7-1" "53-1" "7-2" ...
#> # A tibble: 152 × 5
#>    from  to    birth_year capture_year sampled
#>    <chr> <chr>      <int>        <int> <lgl>  
#>  1 55-1  7-1           20           20 TRUE   
#>  2 53-1  7-2           20           20 TRUE   
#>  3 58-2  8-1           20           20 TRUE   
#>  4 56-2  8-2           20           20 TRUE   
#>  5 73-1  15-1          20           20 TRUE   
#>  6 72-1  15-2          20           20 TRUE   
#>  7 14-2  16-1          20           20 TRUE   
#>  8 75-1  16-2          20           20 TRUE   
#>  9 38-2  3-1           19           19 TRUE   
#> 10 13-1  3-2           19           19 TRUE   
#> # ℹ 142 more rows