Define the genome of a population

Lays out the loci of a population opened with open_pop(): how many, on which chromosomes, at which physical and genetic positions. It is the second step of every simulation, and runs once per population:

pop <- open_pop(pop_name = "pigs", db_name = ":memory:") |>
  define_genome(n_loci = 50000, n_chr = 18, chr_len_Mb = 100)

Next come define_chromosome() for any sex chromosomes or organelles, define_founder_haplotypes() for the founder allele pool, and add_founders().

Usage

define_genome(
  pop,
  n_loci,
  n_chr,
  chr_len_Mb,
  cM_per_Mb = 1,
  locus_names = NULL,
  chr_names = NULL,
  recombines_M = TRUE,
  recombines_F = TRUE
)

Arguments

pop: A tidybreed_pop from open_pop() with no genome yet; define_genome() is refused on a population that already has one.
n_loci: Whole number: the total number of loci (SNPs) across the genome, at least n_chr.
n_chr: Whole number: the number of chromosomes, including any sex chromosomes or organelles you will set up with define_chromosome().
chr_len_Mb: Chromosome length(s) in megabases: one number for every chromosome, or a vector of n_chr values in chromosome order. Sets the physical positions, and with cM_per_Mb the genetic map. It does not change how many loci a chromosome gets.
cM_per_Mb: Recombination rate in centiMorgans per megabase: one number, or a vector of n_chr values. Must be positive. Default 1, about one crossover per 100 Mb per meiosis.
locus_names: Optional character vector of n_loci unique, non-empty names, in genome order (chromosome 1 first). NULL (default) gives "Locus_1", "Locus_2", ...
chr_names: Optional vector of n_chr unique, non-empty chromosome names, in order, e.g. c(1:18, "X", "Y") (stored as text). NULL (default) gives "1", "2", ... Name sex chromosomes and organelles here so define_chromosome() can refer to them.
recombines_M, recombines_F: Logical: whether a male (M) or female (F) parent recombines its chromosomes when making gametes, genome-wide. Both default TRUE. Set one to FALSE for a species where one sex has no crossing over at all, e.g. recombines_M = FALSE for Drosophila males or recombines_F = FALSE for silkworm females. For single chromosomes (a Y or W), use define_chromosome() instead.

Value

The tidybreed_pop, with the genome tables added.

Details

Where the loci go. Loci are divided as evenly as possible across the chromosomes, whatever their lengths (50 loci on 3 chromosomes gives 17, 16, 17), and spaced evenly within each chromosome, never at either end. Each gets an id (locus_id, 1 to n_loci in genome order), a name, a chromosome and a physical position pos_bp, stored in genome_meta. To make some of them QTL or markers later, filter get_table(pop, "genome_meta") and pipe it into define_additive_effects(), define_genome_effects() or define_chip().

Genetic map and recombination. Each locus's genetic position is pos_cM = pos_bp / 1e6 * cM_per_Mb, stored in genome_map. In add_offspring() a chromosome's number of crossovers per meiosis is Poisson with mean equal to its genetic length in Morgans (the last locus's pos_cM / 100), placed uniformly in cM (the Haldane model). So the default 1 cM/Mb gives a 100 Mb chromosome about one crossover per meiosis.

What is created. define_genome() writes genome_meta, genome_map, the seeded chromosome rules chr_inheritance and chr_recombination, and the empty tables later functions fill: ind_haplotype (alleles, written by add_founders() and add_offspring()), ind_genotype (dosages, filled on demand by add_dosage()), ind_crossover and the three genome-effect tables with their views genome_effect_terms and genome_effect_loci. Every chromosome starts as a diploid autosome: one copy from each parent, recombining in both sexes unless recombines_M / recombines_F say otherwise.

The call is atomic: everything is written in one transaction, so an error (an invalid argument, loci too dense to place) leaves the database as it was and you can simply call again with corrected arguments.

Examples

# 1,000 loci on 10 chromosomes of 100 Mb each
pop <- open_pop(pop_name = "A", db_name = ":memory:") |>
  define_genome(n_loci = 1000, n_chr = 10, chr_len_Mb = 100)
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/RtmpvvfSjW/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.
#> Opened in-memory population 'A'
#> Defined genome: 1000 loci across 10 chromosomes | chr lengths (Mb): all equal to 100 Mb
#>   Tables written: genome_meta, genome_map, ind_haplotype, ind_genotype, ind_crossover, chr_inheritance, chr_recombination, genome_effects, genome_effect_members, genome_effect_member_origins
#>   Views created: genome_effect_terms, genome_effect_loci
get_table(pop, "genome_meta")
#> <tidybreed_table: genome_meta>  [1000 rows × 5 fields]
#> # A tibble: 10 × 5
#>    locus_id locus_name   chr chr_name  pos_bp
#>       <int> <chr>      <int> <chr>      <dbl>
#>  1        1 Locus_1        1 1         990099
#>  2        2 Locus_2        1 1        1980198
#>  3        3 Locus_3        1 1        2970297
#>  4        4 Locus_4        1 1        3960396
#>  5        5 Locus_5        1 1        4950495
#>  6        6 Locus_6        1 1        5940594
#>  7        7 Locus_7        1 1        6930693
#>  8        8 Locus_8        1 1        7920792
#>  9        9 Locus_9        1 1        8910891
#> 10       10 Locus_10       1 1        9900990
get_table(pop, "genome_map")
#> <tidybreed_table: genome_map>  [1000 rows × 7 fields]
#> # A tibble: 10 × 7
#>    id_genome_map locus_id locus_name sex   line_name map_name pos_cM
#>            <int>    <int> <chr>      <chr> <chr>     <chr>     <dbl>
#>  1             1        1 Locus_1    NA    NA        default   0.990
#>  2             2        2 Locus_2    NA    NA        default   1.98 
#>  3             3        3 Locus_3    NA    NA        default   2.97 
#>  4             4        4 Locus_4    NA    NA        default   3.96 
#>  5             5        5 Locus_5    NA    NA        default   4.95 
#>  6             6        6 Locus_6    NA    NA        default   5.94 
#>  7             7        7 Locus_7    NA    NA        default   6.93 
#>  8             8        8 Locus_8    NA    NA        default   7.92 
#>  9             9        9 Locus_9    NA    NA        default   8.91 
#> 10            10       10 Locus_10   NA    NA        default   9.90 
close_pop(pop)

# Chromosomes of different lengths, a higher recombination rate and
# your own names (the first three cattle autosomes plus X)
pop <- open_pop(pop_name = "B", db_name = ":memory:") |>
  define_genome(n_loci = 400, n_chr = 4,
                chr_len_Mb = c(158, 137, 121, 139),
                cM_per_Mb  = 1.2,
                chr_names  = c("1", "2", "3", "X"))
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/RtmpvvfSjW/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.
#> Opened in-memory population 'B'
#> Defined genome: 400 loci across 4 chromosomes | chr lengths (Mb): 1:158, 2:137, 3:121, X:139
#>   Tables written: genome_meta, genome_map, ind_haplotype, ind_genotype, ind_crossover, chr_inheritance, chr_recombination, genome_effects, genome_effect_members, genome_effect_member_origins
#>   Views created: genome_effect_terms, genome_effect_loci
close_pop(pop)

# The usual next steps: a founder pool, then founders
set.seed(1)
pop <- open_pop(pop_name = "C", db_name = ":memory:") |>
  define_genome(n_loci = 1000, n_chr = 10, chr_len_Mb = 100) |>
  define_founder_haplotypes(n_haplotypes = 100,
                            min_allele_freq = 0.05,
                            max_allele_freq = 0.95)
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/RtmpvvfSjW/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.
#> Opened in-memory population 'C'
#> Defined genome: 1000 loci across 10 chromosomes | chr lengths (Mb): all equal to 100 Mb
#>   Tables written: genome_meta, genome_map, ind_haplotype, ind_genotype, ind_crossover, chr_inheritance, chr_recombination, genome_effects, genome_effect_members, genome_effect_member_origins
#>   Views created: genome_effect_terms, genome_effect_loci
#> Generating 100 founder haplotypes (method = "uniform")...
#>   Created founder_haplotypes (100 haplotypes x 1000 loci)
pop <- pop |>
  get_table("founder_haplotypes") |>
  add_founders(n_males = 10, n_females = 10, line_name = "A")
#> Added 20 founders (10 males, 10 females) to line 'A'
close_pop(pop)

# No crossing over in males on any chromosome (Drosophila); a single
# non-recombining chromosome goes through define_chromosome() instead
pop <- open_pop(pop_name = "fly", db_name = ":memory:") |>
  define_genome(n_loci = 400, n_chr = 4, chr_len_Mb = c(23, 46, 50, 1.4),
                recombines_M = FALSE)
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/RtmpvvfSjW/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.
#> Opened in-memory population 'fly'
#> Defined genome: 400 loci across 4 chromosomes | chr lengths (Mb): 1:23, 2:46, 3:50, 4:1.4
#>   Tables written: genome_meta, genome_map, ind_haplotype, ind_genotype, ind_crossover, chr_inheritance, chr_recombination, genome_effects, genome_effect_members, genome_effect_member_origins
#>   Views created: genome_effect_terms, genome_effect_loci
get_table(pop, "chr_recombination")
#> <tidybreed_table: chr_recombination>  [8 rows × 4 fields]
#> # A tibble: 8 × 4
#>   chr_name parent_sex line_name recombines
#>   <chr>    <chr>      <chr>     <lgl>     
#> 1 1        M          NA        FALSE     
#> 2 1        F          NA        TRUE      
#> 3 2        M          NA        FALSE     
#> 4 2        F          NA        TRUE      
#> 5 3        M          NA        FALSE     
#> 6 3        F          NA        TRUE      
#> 7 4        M          NA        FALSE     
#> 8 4        F          NA        TRUE      
close_pop(pop)

Usage

Arguments

Value

Details

See also

Examples