Contents

schemaSingleVariant

Association schema for single-variant (GWAS) summary rows ("single.variant")

Column and artifact contract for single-variant scan results. Columns use GWAS naming (chr, position, ea, nea, beta) rather than the regression core.

Usage

schemaSingleVariant()

Value

A PolyGeniusSchema for the "single.variant" analysis type.

Columns

Column	Status	Type	Meaning
`schema`	required	character	Name of the schema the row follows.
`family`	required	character	Fitted regression or comparison family.
`outcome`	required	character	Outcome label.
`genotype`	required	character	Genotype dataset the row belongs to.
`stratum`	required	character	Stratum the fit was run in.
`chr`	required	character	Chromosome, in the package-canonical code (`chr1` to `chr22`, `chrX`, `chrY`, `chrMT`).
`position`	required	integer	Base-pair position.
`variant.id`	required	character	Variant identifier.
`ea`	required	character	Effect (tested) allele.
`nea`	required	character	Non-effect (reference) allele.
`eaf`	required	numeric	Effect-allele frequency.
`test`	required	character
`effect.scale`	required	character	Scale of `estimate`, one of the controlled `effect.scale` vocabulary.
`beta`	required	numeric	Effect size, on the scale given by `effect.scale`.
`se`	required	numeric	Standard error of the estimate.
`statistic`	required	numeric	Test statistic.
`pval`	required	numeric	Raw p-value.
`adj.pval`	required	numeric	Within-scan p-value adjusted with `p.adjust.method`.
`adj.family.id`	required	integer	Key into `$indices$multiplicity`, the adjustment family `adj.pval` came from.
`lower`	required	numeric	Lower interval bound.
`upper`	required	numeric	Upper interval bound.
`n`	required	numeric	Sample size.
`n.cases`	required	numeric	Number of cases.
`n.controls`	required	numeric	Number of controls.
`reference.level`	required	character	Control level for binary phenotypes.
`lambda.gc`	required	numeric	Per-scan genomic-inflation factor.
`outcome.type`	required	character	Phenotype type.

Artifacts

No artifacts. Allowed plots: manhattan, qq (default manhattan).

Meta-analysis

Role	Columns
Keys	`outcome`, `chr`, `position`, `a1.canonical`, `a2.canonical`, `test`, `effect.scale`, `stratum`
Counts	`n`, `n.cases`, `n.controls`
Means	`eaf`