malariagen_data.af1.Af1.cnv_coverage_calls

Af1.cnv_coverage_calls(region: str | Region | Mapping | List[str | Region | Mapping] | Tuple[str | Region | Mapping, ...], sample_set: str, analysis: str, inline_array: bool = True, chunks: int | str | Tuple[int | str, ...] | Callable[[Tuple[int, ...]], int | str | Tuple[int | str, ...]] = 'ndauto0') → Dataset

Access CNV HMM data from genome-wide CNV discovery and filtering.

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.

sample_setstr

Sample set identifier.

analysisstr

Which coverage calls analysis to use. See the coverage_calls_analysis_ids property for available values.

inline_arraybool, optional, default: True

Passed through to dask from_array().

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: ‘ndauto0’

If ‘auto’ let dask decide chunk size. If ‘native’ use native zarr chunks. 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 target size, e.g., ‘200 MiB’, or a tuple of integers, or a callable which accepts the native chunks as a single argument and returns a valid dask chunks value.

Returns

Dataset

An xarray dataset of CNV alleles and genotypes.