mecfs_bio.build_system.sample_size_spec

Specification of how the sample size (N) of a GWAS should be supplied to downstream analyses.

Most GWAS have a single scalar sample size, but meta-analyses and synthetic GWAS produced by GenomicSEM have a sample size that varies per variant. The two cases are modelled by :class:ScalarSampleSize and :class:PerVariantSampleSize respectively, so that call sites and tasks can branch on a named type rather than passing a bare int and a separate flag.

Classes:

• PerVariantSampleSize –

  The sample size varies per variant and is read from column.

• ScalarSampleSize –

  A single sample size shared by every variant in the GWAS.

Functions:

• coerce_sample_size –

  Wrap a bare int as a :class:ScalarSampleSize for backwards

• per_variant_column –

  The data column holding the per-variant sample size, or None for a

Attributes:

• SampleSizeSpec –

SampleSizeSpec module-attribute

SampleSizeSpec = ScalarSampleSize | PerVariantSampleSize

PerVariantSampleSize

The sample size varies per variant and is read from column.

The column must already be present on the GWAS data (e.g. the per-variant effective sample size of a meta-analysis) and survive sumstats creation.

Attributes:

• column (str) –

column class-attribute instance-attribute

column: str = GWASLAB_SAMPLE_SIZE_COLUMN

ScalarSampleSize

A single sample size shared by every variant in the GWAS.

Attributes:

• n (int) –

n instance-attribute

n: int

coerce_sample_size

coerce_sample_size(
    value: int | SampleSizeSpec,
) -> SampleSizeSpec

Wrap a bare int as a :class:ScalarSampleSize for backwards compatibility with call sites that pass a scalar sample size directly.

Source code in mecfs_bio/build_system/sample_size_spec.py

def coerce_sample_size(value: "int | SampleSizeSpec") -> SampleSizeSpec:
    """Wrap a bare ``int`` as a :class:`ScalarSampleSize` for backwards
    compatibility with call sites that pass a scalar sample size directly."""
    if isinstance(value, int):
        return ScalarSampleSize(value)
    return value

per_variant_column

per_variant_column(value: SampleSizeSpec) -> str | None

The data column holding the per-variant sample size, or None for a scalar sample size (so callers know not to write an N column).

Source code in mecfs_bio/build_system/sample_size_spec.py

def per_variant_column(value: SampleSizeSpec) -> str | None:
    """The data column holding the per-variant sample size, or ``None`` for a
    scalar sample size (so callers know not to write an N column)."""
    if isinstance(value, PerVariantSampleSize):
        return value.column
    return None