malariagen_data.ag3.Ag3.h12_calibration

Ag3.h12_calibration(contig: str, analysis: str = 'default', sample_query: str | None = None, sample_sets: Sequence[str] | str | None = None, cohort_size: int | None = None, min_cohort_size: int | None = 15, max_cohort_size: int | None = 50, window_sizes: Tuple[int, ...] = (100, 200, 500, 1000, 2000, 5000, 10000, 20000), random_seed: int = 42) → Mapping[str, ndarray]

Generate h12 GWSS calibration data for different window sizes.

Parameters

contigstr

Reference genome contig name. See the contigs property for valid contig names.

analysisstr, optional, default: ‘default’

Which haplotype phasing analysis to use. See the phasing_analysis_ids property for available values.

sample_querystr or None, optional

A pandas query string to be evaluated against the sample metadata, to select samples to be included in the returned data.

sample_setssequence of str or str or None, optional

List of sample sets and/or releases. Can also be a single sample set or release.

cohort_sizeint or None, optional

Randomly down-sample to this value if the number of samples in the cohort is greater. Raise an error if the number of samples is less than this value.

min_cohort_sizeint or None, optional, default: 15

Minimum cohort size. Raise an error if the number of samples is less than this value.

max_cohort_sizeint or None, optional, default: 50

Randomly down-sample to this value if the number of samples in the cohort is greater.

window_sizestuple of int, optional, default: (100, 200, 500, 1000, 2000, 5000, 10000, 20000)

The sizes of windows (number of SNPs) used to calculate statistics within.

random_seedint, optional, default: 42

Random seed used for reproducible down-sampling.

Returns

Mapping[str, ndarray]

A list of H12 calibration run arrays for each window size, containing values and percentiles.