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Compare Haplotype Allele Frequencies Between Two Population Groups

Source: R/haplotype_analysis.R
compare_haplotype_populations.Rd

For each LD block, computes allele frequencies in two sample groups and returns FST (Weir-Cockerham 1984), frequency differences, and a chi-squared test of independence. Useful for detecting blocks under divergent selection or monitoring diversity changes between breeding cycles.

Usage

compare_haplotype_populations(
  haplotypes,
  group1,
  group2,
  group1_name = "group1",
  group2_name = "group2",
  min_freq = 0.02,
  missing_string = "."
)

Arguments

haplotypes

Named list from extract_haplotypes.

group1

Character vector of individual IDs for group 1 (e.g. wild/landrace accessions).

group2

Character vector of individual IDs for group 2 (e.g. elite breeding lines).

group1_name

Character. Label for group 1. Default "group1".

group2_name

Character. Label for group 2. Default "group2".

min_freq

Numeric. Alleles below this frequency in both groups are pooled into an "other" category before testing. Default 0.02.

missing_string

Character. Missing haplotype placeholder. Default ".".

Value

Data frame with one row per block, sorted by CHR and start_bp.

block_id, CHR, start_bp, end_bp

Block coordinates.

n1, n2

Sample sizes for group 1 and group 2.

n_alleles

Number of distinct alleles in this block.

FST

Weir-Cockerham FST, clamped to [0,1].

max_freq_diff

Maximum absolute allele frequency difference.

dominant_g1, dominant_g2

Most frequent allele in each group.

chisq_p

Chi-squared p-value (Monte Carlo). NA if < 2 alleles.

divergent

Logical; TRUE when FST > 0.1 and chisq_p < 0.05.

References

Weir BS, Cockerham CC (1984). Estimating F-statistics for the analysis of population structure. Evolution 38(6):1358-1370.

See also

extract_haplotypes, compute_haplotype_diversity

Examples

# \donttest{
data(ldx_geno, ldx_snp_info, ldx_blocks, package = "LDxBlocks")
haps <- extract_haplotypes(ldx_geno, ldx_snp_info, ldx_blocks)
ids  <- rownames(ldx_geno)
cmp  <- compare_haplotype_populations(
  haplotypes   = haps,
  group1       = ids[1:60],
  group2       = ids[61:120],
  group1_name  = "cycle1",
  group2_name  = "cycle2"
)
cmp[cmp$divergent, c("block_id", "FST", "max_freq_diff", "chisq_p")]
#> [1] block_id      FST           max_freq_diff chisq_p      
#> <0 rows> (or 0-length row.names)
# }