plink_ld¶

Compute pairwise linkage disequilibrium statistics (r², D').

Synopsis¶

-- Pairwise mode: LD between two specific variants
plink_ld(path VARCHAR, variant1 := ..., variant2 := ...) -> TABLE

-- Windowed mode: LD for all variant pairs within a window
plink_ld(path VARCHAR [, window_kb := ..., r2_threshold := ...,
         region := ..., samples := ..., inter_chr := ...]) -> TABLE

Parameters¶

Name	Type	Default	Description
`path`	`VARCHAR`	(required)	Path to the `.pgen` file
`pvar`	`VARCHAR`	Auto-discovered	Path to `.pvar` or `.bim` file
`psam`	`VARCHAR`	Auto-discovered	Path to `.psam` or `.fam` file
`variant1`	`VARCHAR`	(none)	First variant ID (pairwise mode)
`variant2`	`VARCHAR`	(none)	Second variant ID (pairwise mode)
`window_kb`	`INTEGER`	`1000`	Window size in kilobases (windowed mode)
`r2_threshold`	`DOUBLE`	`0.2`	Minimum r² to report (windowed mode)
`samples`	`LIST(VARCHAR)` or `LIST(INTEGER)`	All	Subset to specific samples
`region`	`VARCHAR`	All	Filter to genomic region (`chr:start-end`)
`inter_chr`	`BOOLEAN`	`false`	Include cross-chromosome pairs (windowed mode)

See Common Parameters for details on pvar, psam, samples, and region.

Modes¶

Pairwise Mode¶

When both variant1 and variant2 are specified, the function computes LD for that single pair and returns exactly one row. Both variant IDs must exist in the .pvar file.

Windowed Mode¶

When neither variant1 nor variant2 is specified, the function scans all variant pairs within a sliding window. For each anchor variant, it tests all subsequent variants within window_kb kilobases on the same chromosome and reports pairs where r² >= r2_threshold.

With inter_chr := true, cross-chromosome pairs are also tested (no distance filter applies across chromosomes).

Output Columns¶

Column	Type	Description
`CHROM_A`	`VARCHAR`	Chromosome of first variant
`POS_A`	`INTEGER`	Position of first variant
`ID_A`	`VARCHAR`	ID of first variant
`CHROM_B`	`VARCHAR`	Chromosome of second variant
`POS_B`	`INTEGER`	Position of second variant
`ID_B`	`VARCHAR`	ID of second variant
`R2`	`DOUBLE`	Squared correlation coefficient (NULL if invalid)
`D_PRIME`	`DOUBLE`	Normalized linkage disequilibrium coefficient (NULL if invalid)
`OBS_CT`	`INTEGER`	Number of samples with non-missing genotypes at both variants

R2 and D_PRIME are NULL when the LD computation is invalid (monomorphic variants, fewer than 2 shared observations).

Description¶

LD Statistics¶

r² is the squared Pearson correlation between genotype dosages at two loci. Values range from 0 (no LD) to 1 (perfect LD).

D' is computed using the composite LD estimator (Weir 1979) from genotype-level statistics. D is the covariance between genotype dosages divided by 4, and D' = D / D_max where D_max depends on allele frequencies and the sign of D.

Note

Because this uses genotype-level (not haplotype-level) statistics, D' can exceed 1.0 when samples deviate from Hardy-Weinberg equilibrium.

Invalid Results¶

LD statistics are NULL when:

Either variant is monomorphic (zero variance)
Fewer than 2 samples have non-missing genotypes at both loci

Parallel Scan¶

Windowed mode supports multi-threaded scanning where each thread claims anchor variants independently.

Examples¶

-- Pairwise LD between two variants
SELECT * FROM plink_ld('data/example.pgen',
    variant1 := 'rs1', variant2 := 'rs2');

-- Windowed LD with default parameters (1000kb window, r² >= 0.2)
SELECT * FROM plink_ld('data/example.pgen');

-- Narrow window with lower threshold
SELECT * FROM plink_ld('data/example.pgen',
    window_kb := 250, r2_threshold := 0.05);

-- LD in a specific region
SELECT * FROM plink_ld('data/example.pgen',
    region := '1:1-1000000');

-- Include cross-chromosome LD
SELECT * FROM plink_ld('data/example.pgen',
    inter_chr := true, r2_threshold := 0.8);