malariagen_data.af1.Af1.diversity_stats

Af1.diversity_stats(cohorts: str | Mapping[str, str], cohort_size: int, region: str | Region | Mapping | List[str | Region | Mapping] | Tuple[str | Region | Mapping, ...], site_mask: str | None = 'default', site_class: str | None = None, sample_query: str | None = None, sample_sets: Sequence[str] | str | None = None, random_seed: int = 42, n_jack: int = 200, confidence_level: float = 0.95) → DataFrame

Compute genetic diversity summary statistics for multiple cohorts.

Parameters

cohortsstr or Mapping[str, str]

Either a string giving the name of a predefined cohort set (e.g., “admin1_month”) or a dict mapping custom cohort labels to sample queries.

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.

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_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.

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.

Returns

DataFrame

A DataFrame where each row provides summary statistics and their confidence intervals for a single cohort.