malariagen_data.ag3.Ag3.gene_cnv_frequencies

Ag3.gene_cnv_frequencies(region: str | Region | Mapping | List[str | Region | Mapping] | Tuple[str | Region | Mapping, ...], cohorts: str | Mapping[str, str], sample_query: str | None = None, sample_query_options: dict | None = None, min_cohort_size: int = 10, max_coverage_variance: float | None = 0.2, sample_sets: Sequence[str] | str | None = None, drop_invariant: bool = True, include_counts: bool = False, chunks: int | str | Tuple[int | str, ...] | Callable[[Tuple[int, ...]], int | str | Tuple[int | str, ...]] = 'native', inline_array: bool = True) → DataFrame

Compute modal copy number by gene, then compute the frequency of amplifications and deletions in one or more cohorts, from HMM data.

Parameters

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.

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_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.

min_cohort_sizeint, optional, default: 10

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

max_coverage_variancefloat or None, optional, default: 0.2

Remove samples if coverage variance exceeds this value.

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.

drop_invariantbool, optional, default: True

If True, drop variants not observed in the selected samples.

include_countsbool, optional, default: False

Include columns with allele counts and number of non-missing allele calls (nobs).

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

DataFrame

A dataframe of CNV amplification (amp) and deletion (del) frequencies in the specified cohorts, one row per gene and CNV type (amp/del).