malariagen_data.af1.Af1.h1x_gwss

Af1.h1x_gwss(contig: str, window_size: int, cohort1_query: str, cohort2_query: str, sample_query_options: dict | None = None, analysis: str = 'default', sample_sets: Sequence[str] | str | None = None, cohort_size: int | None = None, min_cohort_size: int | None = 15, max_cohort_size: int | None = 50, random_seed: int = 42, chunks: int | str | Tuple[int | str, ...] | Callable[[Tuple[int, ...]], int | str | Tuple[int | str, ...]] = 'native', inline_array: bool = True) → Tuple[ndarray, ndarray, ndarray]

Run a H1X genome-wide scan to detect genome regions with shared selective sweeps 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 SNPs) 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_query_optionsdict or None, optional

A dictionary of arguments that will be passed through to pandas query() or eval(), e.g. parser, engine, local_dict, global_dict, resolvers.

analysisstr, optional, default: ‘default’

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

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.

random_seedint, optional, default: 42

Random seed used for reproducible down-sampling.

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

Define how input data being read from zarr should be divided into chunks for a dask computation. If ‘native’, use underlying zarr chunks. If a string specifying a target memory size, e.g., ‘300 MiB’, resize chunks in arrays with more than one dimension to match this size. If ‘auto’, let dask decide chunk size. If ‘ndauto’, let dask decide chunk size but only for arrays with more than one dimension. If ‘ndauto0’, as ‘ndauto’ but only vary the first chunk dimension. If ‘ndauto1’, as ‘ndauto’ but only vary the second chunk dimension. If ‘ndauto01’, as ‘ndauto’ but only vary the first and second chunk dimensions. Also, can be a tuple of integers, or a callable which accepts the native chunks as a single argument and returns a valid dask chunks value.

inline_arraybool, optional, default: True

Passed through to dask from_array().

Returns

xndarray

An array containing the window centre point genomic positions.

h1xndarray

An array with H1X statistic values for each window.

contigsndarray

An array with the contig for each window. The median is chosen for windows overlapping a change of contig.