Function Reference¶

PlinkingDuck provides 11 SQL table functions: 5 file readers and 6 analysis functions.

File Readers¶

Function	Input	Description
`read_pvar(path)`	`.pvar` / `.bim`	Variant metadata (CHROM, POS, ID, REF, ALT)
`read_psam(path)`	`.psam` / `.fam`	Sample metadata (FID, IID, SEX, phenotypes)
`read_pgen(path)`	`.pgen`	Binary genotypes as `ARRAY(TINYINT, N)`
`read_pfile(prefix)`	`.pgen` + `.pvar` + `.psam`	Complete fileset with orient mode support
`read_plink_vcf(path)`	`.vcf` / `.vcf.gz`	Fast biallelic genotype extraction from VCF

Analysis Functions¶

Function	Input	Description
`plink_freq(path)`	`.pgen`	Per-variant allele frequencies and genotype counts
`plink_hardy(path)`	`.pgen`	Hardy-Weinberg equilibrium exact test p-values
`plink_missing(path)`	`.pgen`	Per-variant or per-sample missingness rates
`plink_ld(path)`	`.pgen`	Pairwise linkage disequilibrium (r², D')
`plink_score(path)`	`.pgen`	Polygenic risk scoring
`plink_glm(prefix)`	pfile prefix	Per-variant GWAS regression (linear, logistic, Firth)

Common Features¶

All functions support projection pushdown: columns not referenced in the query are not computed. For genotype-based functions, this means metadata-only queries skip genotype decoding entirely.

Analysis functions (except plink_ld) share a common set of named parameters documented in Common Parameters: pvar, psam, samples, and region.