malariagen_data.ag3.Ag3.cohort_diversity_stats

Ag3.cohort_diversity_stats(cohort: str | Tuple[str, str], cohort_size: int, region: str | Region | Mapping | List[str | Region | Mapping] | Tuple[str | Region | Mapping, ...], min_cohort_size: int | None = None, max_cohort_size: int | None = None, site_mask: str | None = 'default', site_class: str | None = None, sample_sets: Sequence[str] | str | None = None, random_seed: int = 42, n_jack: int = 200, confidence_level: float = 0.95, chunks: int | str | Tuple[int | str, ...] | Callable[[Tuple[int, ...]], int | str | Tuple[int | str, ...]] = 'native', inline_array: bool = True) → Series

Compute genetic diversity summary statistics for a cohort of individuals.

Parameters

cohortstr or tuple[str, str]

Either a string giving one of the predefined cohort labels, or a pair of strings giving a custom cohort label and a sample query.

cohort_sizeint

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.

regionstr or Region or Mapping or list of str or Region or Mapping or tuple of str or Region or Mapping

Region of the reference genome. Can be a contig name, region string (formatted like “{contig}:{start}-{end}”), or identifier of a genome feature such as a gene or transcript. Can also be a sequence (e.g., list) of regions.

min_cohort_sizeint or None, optional

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

max_cohort_sizeint or None, optional

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

site_maskstr or None, optional, default: ‘default’

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

site_classstr or None, optional

Select sites belonging to one of the following classes: CDS_DEG_4, (4-fold degenerate coding sites), CDS_DEG_2_SIMPLE (2-fold simple degenerate coding sites), CDS_DEG_0 (non-degenerate coding sites), INTRON_SHORT (introns shorter than 100 bp), INTRON_LONG (introns longer than 200 bp), INTRON_SPLICE_5PRIME (intron within 2 bp of 5’ splice site), INTRON_SPLICE_3PRIME (intron within 2 bp of 3’ splice site), UTR_5PRIME (5’ untranslated region), UTR_3PRIME (3’ untranslated region), INTERGENIC (intergenic, more than 10 kbp from a gene).

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.

random_seedint, optional, default: 42

Random seed used for reproducible down-sampling.

n_jackint, optional, default: 200

Number of blocks to divide the data into for the block jackknife estimation of confidence intervals. N.B., larger is not necessarily better.

confidence_levelfloat, optional, default: 0.95

Confidence level to use for confidence interval calculation. E.g., 0.95 means 95% confidence interval.

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

Series

A pandas series with summary statistics (theta pi, Watterson’s theta and Tajima’s D) and their estimate, bias, standard error, confidence interval error, confidence interval lower value, and confidence interval upper value. The series also contains the cohort under study, its taxon, its year of collection, its month of collection, its country of collection, the ISO code of its first administrative level of collection, the name of its first administrative level of collection, the name of its second administrative level of collection, the longitude of its location of collection, and the latitude of its location of collection.