Today our new R package hiphop (developed together with my colleagues Lyanne Brouwer & Andrew Cockburn) was published online by CRAN.
No, my music taste is not developing, I still stick to my good-old rock music preference. Instead, this package contains several functions to easily perform parentage analysis using bi-allelic genetic markers such as SNPs. It outperforms conventional methods where closely related individuals occur in the pool of possible parents. The method compares the genotypes of offspring with any combination of potentials parents and scores the number of genetic mismatches of these individuals at different loci. It elaborates on a prior exclusion method based on the Homozygous Opposite Test (HOT; Huisman 2017) by introducing the additional exclusion criterion HIPHOP (Homozygous Identical Parents, Heterozygous Offspring are Precluded; Cockburn et al., in revision). Potential parents are excluded if they have more mismatches than can be expected due to genotyping error and mutation, and thereby one can identify the true genetic parents and detect situations where one (or both) of the true parents is not sampled. Package ‘hiphop’ can deal with (a) the case where there is contextual information about parentage of the mother (i.e. a female has been seen to be involved in reproductive tasks such as nest building), but paternity is unknown (e.g. due to promiscuity), (b) where both parents need to be assigned, because there is no contextual information on which female laid eggs and which male fertilized them (e.g. polygynandrous mating system where multiple females and males deposit young in a common nest, or organisms with external fertilisation that breed in aggregations).
We hope to publish the accompaning scientific paper very soon!