Heterozygosity Blue #335
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Heterozygosity Blue #335
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This function calculates expected heterozygosity with a correction for relatedness of individuals based on a kinship matrix. In this implementation the kinship matrix is an optional argument an if it is not present then the 'typical' expected heterozygosity is calculated which is equivilent to heterozygosity_blue with unrelated individuals. This function is also suitable for mixed ploidy data.
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Best linear unbiased estimate of expected heterozygosity following eq. 8 in Harris and DeGiorgio (2017).
Heterozygosity_blue is a variation of heterozygosity_expected which minimizes bias due to related individuals based on a kniship matrix.
This implementation makes the kinship matrix an optional argument.
If kinship is not specified then "regular" heterozygosity_expected is calculated using the (n / (n-1)) correction
described in #145 (resolving that issue).
This is a sensible 'default' because heterozygosity_blue is equivalent to heterozygosity_expected when the kinship matrix indicates non-related, non-inbred individuals (a matrix of zeros with a diagonal of 1/ploidy).
The implementation is a little more complex than ideal because the inverse of the kinship matrix must be calculated for only the called samples at each variant.
I have tried to do this in a way that minimizes recalculation of the inverse matrix.
Additionally a nan value is returned if the (sub-)kinship matrix has no inverse.
It's worth noting that heterozygosity_blue can return values outside of the interval [0, 1] with some inputs.
Related to #287 there is an optional argument to specify mixed ploidy data