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plink_hardy

Compute per-variant Hardy-Weinberg equilibrium exact test p-values.

Synopsis

plink_hardy(path VARCHAR [, pvar := ..., psam := ..., samples := ...,
            region := ..., midp := ...]) -> 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
samples LIST(VARCHAR) or LIST(INTEGER) All Subset to specific samples
region VARCHAR All Filter to genomic region (chr:start-end)
midp BOOLEAN false Use mid-p correction for the exact test

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

Output Columns

Column Type Description
CHROM VARCHAR Chromosome
POS INTEGER Base-pair position
ID VARCHAR Variant identifier
REF VARCHAR Reference allele
ALT VARCHAR Alternate allele
A1 VARCHAR Tested allele (the alternate allele)
HOM_REF_CT INTEGER Homozygous reference count
HET_CT INTEGER Heterozygous count
HOM_ALT_CT INTEGER Homozygous alternate count
O_HET DOUBLE Observed heterozygosity (NULL if no observations)
E_HET DOUBLE Expected heterozygosity under HWE (NULL if no observations)
P_HWE DOUBLE HWE exact test p-value (NULL if no observations)

Description

plink_hardy performs a Hardy-Weinberg equilibrium exact test for each variant, implementing the algorithm described by Wigginton et al. (2005). The test enumerates all valid heterozygote counts for fixed allele counts and computes p-values by summing probabilities of configurations as likely or less likely than observed.

Heterozygosity

  • O_HET (observed): HET_CT / (HOM_REF_CT + HET_CT + HOM_ALT_CT)
  • E_HET (expected): 2 * p * q where p = (2*HOM_REF_CT + HET_CT) / (2*total) and q = 1 - p

Mid-p Correction

When midp := true, the p-value is adjusted by subtracting half the probability of the observed configuration. This reduces conservativeness of the exact test and is recommended for large sample sizes.

Projection Pushdown

If only metadata columns (CHROM through ALT) are selected, genotype counting and the HWE test are skipped.

Examples

-- Basic HWE test
SELECT * FROM plink_hardy('data/example.pgen');

-- With mid-p correction
SELECT ID, P_HWE
FROM plink_hardy('data/example.pgen', midp := true);

-- QC filter: find variants failing HWE
SELECT ID, P_HWE, O_HET, E_HET
FROM plink_hardy('data/example.pgen')
WHERE P_HWE < 1e-6;

-- HWE test restricted to a region
SELECT ID, P_HWE
FROM plink_hardy('data/example.pgen',
    region := '1:1-50000000');

-- HWE test in a sample subset (e.g., controls only)
SELECT ID, P_HWE
FROM plink_hardy('data/example.pgen',
    samples := ['CTRL1', 'CTRL2', 'CTRL3']);

See Also