malariagen_data.af1.Af1.gene_cnv_frequencies

Af1.gene_cnv_frequencies(region: str | Region | Mapping | List[str | Region | Mapping] | Tuple[str | Region | Mapping, ...], cohorts, sample_query=None, min_cohort_size=10, sample_sets=None, drop_invariant=True, max_coverage_variance=0.2)

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

Parameters

region: str or list of str or Region or list of Region

Chromosome arm (e.g., “2L”), gene name (e.g., “AGAP007280”), genomic region defined with coordinates (e.g., “2L:44989425-44998059”) or a named tuple with genomic location Region(contig, start, end). Multiple values can be provided as a list, in which case data will be concatenated, e.g., [“3R”, “3L”].

cohortsstr or dict

If a string, gives the name of a predefined cohort set, e.g., one of {“admin1_month”, “admin1_year”, “admin2_month”, “admin2_year”}. If a dict, should map cohort labels to sample queries, e.g., {“bf_2012_col”: “country == ‘Burkina Faso’ and year == 2012 and taxon == ‘coluzzii’”}.

sample_querystr, optional

A pandas query string which will be evaluated against the sample metadata e.g., “taxon == ‘coluzzii’ and country == ‘Burkina Faso’”.

min_cohort_sizeint

Minimum cohort size, below which cohorts are dropped.

sample_setsstr or list of str, optional

Can be a sample set identifier (e.g., “AG1000G-AO”) or a list of sample set identifiers (e.g., [“AG1000G-BF-A”, “AG1000G-BF-B”]) or a release identifier (e.g., “3.0”) or a list of release identifiers.

drop_invariantbool, optional

If True, drop any rows where there is no evidence of variation.

max_coverage_variancefloat, optional

Remove samples if coverage variance exceeds this value.

Returns

dfpandas.DataFrame

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