Source code for hail.experimental.filtering_allele_frequency

from hail.expr.expressions import expr_float64, expr_int32, Float64Expression
from hail.expr.types import tfloat64
from hail.typecheck import typecheck
from hail.expr.functions import _func

[docs]@typecheck(ac=expr_int32, an=expr_int32, ci=expr_float64) def filtering_allele_frequency(ac, an, ci) -> Float64Expression: """ Computes a filtering allele frequency (described below) for `ac` and `an` with confidence `ci`. The filtering allele frequency is the highest true population allele frequency for which the upper bound of the `ci` (confidence interval) of allele count under a Poisson distribution is still less than the variant’s observed `ac` (allele count) in the reference sample, given an `an` (allele number). This function defines a "filtering AF" that represents the threshold disease-specific "maximum credible AF" at or below which the disease could not plausibly be caused by that variant. A variant with a filtering AF >= the maximum credible AF for the disease under consideration should be filtered, while a variant with a filtering AF below the maximum credible remains a candidate. This filtering AF is not disease-specific: it can be applied to any disease of interest by comparing with a user-defined disease-specific maximum credible AF. For more details, see: `Whiffin et al., 2017 <>`__ Parameters ---------- ac : int or :class:`.Expression` of type :py:data:`.tint32` an : int or :class:`.Expression` of type :py:data:`.tint32` ci : float or :class:`.Expression` of type :py:data:`.tfloat64` Returns ------- :class:`.Expression` of type :py:data:`.tfloat64` """ return _func("filtering_allele_frequency", tfloat64, ac, an, ci)