malariagen_data.af1.Af1.cnv_hmm

Af1.cnv_hmm(region: str | Region | Mapping | List[str | Region | Mapping] | Tuple[str | Region | Mapping, ...], sample_sets: Sequence[str] | str | None = None, sample_query: str | None = None, sample_query_options: dict | None = None, max_coverage_variance: float | None = 0.2, inline_array: bool = True, chunks: int | str | Tuple[int | str, ...] | Callable[[Tuple[int, ...]], int | str | Tuple[int | str, ...]] = 'native') → Dataset

Access CNV HMM data from CNV calling.

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_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.

max_coverage_variancefloat or None, optional, default: 0.2

Remove samples if coverage variance exceeds this value.

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: ‘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.

Returns

Dataset

A dataset with 2 dimensions: variants the number of CNV regions in the selected region, samples the number of samples. There are 4 coordinates: variant_position has variants values and contains the initial position of each CNV region, variant_end has variants values and contains the final position of each CNV region, variant_contig has variants values and contains the contig of each CNV region, sample_id has samples values and contains the identifier of each sample. It contains 5 data variables: call_CN, it has (variants, samples) values and contains the number of copies for each sample and each CNV region, call_RawCov, it has (variants, samples) values and contains the raw coverage for each sample and each CNV region, call_NormCov, it has (variants, samples) values and contains the normalized coverage for each sample and each CNV region, sample_coverage_variance, it has samples values and contains the variance of the coverage for each sample, sample_id_high_variance, it has samples values and contains whether each sample has a high variance.