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Trans mapping¤

jaxqtl supports trans-eQTL mapping by streaming genotype variants in chunks and testing each variant against many phenotypes.

Chunked scanning¤

Trans scans can be large (millions of variants times thousands of phenotypes). jaxqtl supports streaming:

  • iterate over genotype blocks of size chunk_size
  • compute association statistics for all phenotypes in each block
  • write or post-process block outputs incrementally

Mapping and output schemas¤

jaxqtl.map.map_trans(data: ReadyDataState, test: AbstractHypothesisTest, chunk_size: int = 5000, verbose: bool = True, log: logging.Logger | None = None, seed: int = 123) -> collections.abc.Iterator[tuple[polars.dataframe.frame.DataFrame, polars.dataframe.frame.DataFrame]] ¤

Perform trans-eQTL mapping in genotype chunks and stream results.

Phenotypes with zero or NaN variance are excluded before mapping.

Arguments:

  • data: Genotype/expression/covariate bundle aligned on IID.
  • test: Hypothesis test to apply per variant (score or Wald).
  • chunk_size: Number of variants per block to stream from genotype storage.
  • verbose: Whether to emit progress logging.
  • log: Optional logger to use; defaults to module logger.
  • seed: Reserved for future stochastic operations. It does not affect current trans results.

Returns:

An iterator of (variant_df, sumstat_df) pairs. variant_df contains one row per variant in the block. sumstat_df contains the phenotype-by-variant association results, ordered by phenotype and then variant.

Failure Modes:

If no phenotype has nonzero, non-NaN variance, the iterator yields no results and logs a warning.

jaxqtl.map.get_trans_schemas() -> tuple[dict[str, type], dict[str, type]] ¤

Return column schemas for trans mapping outputs.

Returns:

A tuple (variant_schema, sumstat_schema). The variant schema contains chrom, snp, pos, a1, a0, af, and ma_count. The summary-stat schema contains phenotype, snp, beta, se, pvalue, nb_alpha, and model_converged. Non-Negative-Binomial scans omit nb_alpha from emitted summary-stat frames.