posthoc.qc

class posthoc.qc.filters.QCResult(data: 'GenotypeData', n_dropped_maf: 'int' = 0, n_dropped_geno: 'int' = 0, n_dropped_ld: 'int' = 0)[source]

Bases: object

Parameters:

data (GenotypeData)
n_dropped_maf (int)
n_dropped_geno (int)
n_dropped_ld (int)

data: GenotypeData

n_dropped_maf: int = 0

n_dropped_geno: int = 0

n_dropped_ld: int = 0

summary()[source]

Return type:: str

posthoc.qc.filters.compute_maf(genotypes)[source]

Parameters:: genotypes (ndarray)
Return type:: ndarray

posthoc.qc.filters.compute_missing_rate(genotypes)[source]

Parameters:: genotypes (ndarray)
Return type:: ndarray

posthoc.qc.filters.filter_maf(data, min_maf)[source]

Parameters:

data (GenotypeData)
min_maf (float)

Return type:

tuple[GenotypeData, int]

posthoc.qc.filters.filter_geno(data, max_missing)[source]

Parameters:

data (GenotypeData)
max_missing (float)

Return type:

tuple[GenotypeData, int]

posthoc.qc.filters.indep_pairwise(pfile_prefix, window_size, step, r2_threshold, plink2_path=None)[source]

Parameters:

pfile_prefix (str | Path)
window_size (int)
step (int)
r2_threshold (float)
plink2_path (str | None)

Return type:

list[str]

posthoc.qc.filters.apply_ld_pruning(data, keep_ids)[source]

Parameters:

data (GenotypeData)
keep_ids (list[str])

Return type:

tuple[GenotypeData, int]

posthoc.qc.filters.run_qc(data, *, min_maf=0.0, max_missing=1.0, indep_pairwise_params=None, pfile_prefix=None)[source]

Parameters:

data (GenotypeData)
min_maf (float)
max_missing (float)
indep_pairwise_params (tuple[int, int, float] | None)
pfile_prefix (str | Path | None)

Return type:

QCResult