malariagen_data.ag3.Ag3.pairwise_average_fst

Ag3.pairwise_average_fst(region: str | Region | Mapping, cohorts: str | Mapping[str, str], sample_sets: Sequence[str] | str | None = None, sample_query: str | None = None, sample_query_options: dict | None = None, cohort_size: int | None = None, min_cohort_size: int | None = 15, max_cohort_size: int | None = 50, n_jack: int = 200, site_mask: str | None = 'default', site_class: str | None = None, random_seed: int = 42) → DataFrame

Compute pairwise average Hudson’s Fst between a set of specified cohorts.

Parameters

regionstr 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.

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.

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.

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_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.

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.

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.

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).

random_seedint, optional, default: 42

Random seed used for reproducible down-sampling.

Returns

DataFrame

A dataframe of pairwise Fst and standard error values. It has 4 columns: cohort1 and cohort2 are the two cohorts, fst is the value of the Fst between the two cohorts, se is the standard error.