malariagen_data.ag3.Ag3.fst_gwss

Ag3.fst_gwss(contig: str, window_size: int, cohort1_query: str, cohort2_query: str, sample_sets: Sequence[str] | str | None = None, site_mask: str = 'default', cohort_size: int | None = None, min_cohort_size: int | None = 15, max_cohort_size: int | None = 50, random_seed: int = 42, inline_array: bool = True, chunks: str | Tuple[int, ...] | Callable[[Tuple[int, ...]], Tuple[int, ...]] = 'native') → Tuple[ndarray, ndarray]

Run a Fst genome-wide scan to investigate genetic differentiation between two cohorts.

Parameters

contigstr

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

window_sizeint

The size of windows (number of sites) used to calculate statistics within.

cohort1_querystr

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

cohort2_querystr

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.

site_maskstr, optional, default: ‘default’

Which site filters mask to apply. See the site_mask_ids property for available values.

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.

random_seedint, optional, default: 42

Random seed used for reproducible down-sampling.

inline_arraybool, optional, default: True

Passed through to dask from_array().

chunksstr or tuple of int or Callable[[typing.Tuple[int, …]], tuple of int], optional, default: ‘native’

If ‘auto’ let dask decide chunk size. If ‘native’ use native zarr chunks. Also, can be a target size, e.g., ‘200 MiB’, or a tuple of integers.

Returns

xndarray

An array containing the window centre point genomic positions.

fstndarray

An array with Fst statistic values for each window.