Sliding-Window Genome-Wide Diversity Scan

Computes haplotype diversity metrics (He, Shannon entropy, n_eff_alleles, dominant frequency) in sliding windows across the genome, independently of LD block boundaries. Useful for identifying diversity valleys (bottlenecks, selective sweeps) and comparing wild/elite panels without needing pre-defined blocks.

Usage

scan_diversity_windows(
  geno_matrix,
  snp_info,
  window_bp = 1000000L,
  step_bp = 500000L,
  min_snps_win = 5L,
  missing_val = NA
)

Arguments

geno_matrix

Numeric matrix (individuals x SNPs), 0/1/2/NA.

snp_info

Data frame with SNP, CHR, POS.

window_bp

Integer. Window size in base pairs. Default 1e6L (1 Mb).

step_bp

Integer. Step size in base pairs. Default 5e5L (500 kb, i.e. 50% overlap).

min_snps_win

Integer. Minimum SNPs in a window to compute diversity (windows with fewer are skipped). Default 5L.

missing_val

Numeric. Value representing missing data in geno_matrix. Default NA.

Value

Data frame with one row per sliding window, sorted by CHR then win_start. Columns:

CHR

Chromosome label.

win_start, win_end

Window boundaries (bp).

win_mid

Window midpoint (bp).

n_snps

Number of SNPs in the window.

n_ind

Number of individuals with non-missing data.

n_haplotypes

Number of distinct haplotype strings.

He

Nei (1973) expected heterozygosity, sample-size corrected.

Shannon

Shannon entropy of haplotype frequencies.

n_eff_alleles

Effective number of alleles (1/sum(p_i^2)).

freq_dominant

Frequency of the most common haplotype.

sweep_flag

Logical; TRUE when freq_dominant >= 0.90.

See also

compute_haplotype_diversity, compare_haplotype_populations

Examples

# \donttest{
data(ldx_geno, ldx_snp_info, package = "LDxBlocks")
scan <- scan_diversity_windows(
  geno_matrix  = ldx_geno,
  snp_info     = ldx_snp_info,
  window_bp    = 50000L,
  step_bp      = 25000L,
  min_snps_win = 3L
)
# Plot He across chromosome 1
chr1 <- scan[scan$CHR == "1", ]
plot(chr1$win_mid / 1e3, chr1$He, type = "l",
     xlab = "Position (kb)", ylab = "He",
     main = "Haplotype diversity scan - chr 1")

# }