PMC:4289681 / 23095-23968 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/4289681","sourcedb":"PMC","sourceid":"4289681","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4289681","text":"Inbreeding Estimation\nAdmixture also affects standard estimators of inbreeding coefficients, and we correct for this by allowing for admixture. We estimate the inbreeding coefficient F for each individual with a maximum-likelihood method that uses the estimated admixture proportions α=(α1,α2,…,αK) for the given individual along with the allele frequencies for the K source populations fs=(fs1,fs2,…,fsK) for each site s as estimated by ADMIXTURE.23 Let gs∈(0,1,2) be the individual’s genotype at site s, and let fs∗=∑k=1Kαkfsk be the probability of observing the minor allele at site s. The likelihood of F given the genotype data, D=(g1,g2,…,gS), is then given asL(F)=Pr(D|F)=∏s=1SPr(gs|F)withPr(gs|F)= {(1−fs∗)2(1−F)+(1−fs∗)F, gs=02(1−fs∗)fs∗(1−F),gs=1 fs∗fs∗(1−F)+fs∗F, gs=2\nThe maximum-likelihood estimate of F is then the F value that maximizes the above likelihood.","divisions":[{"label":"title","span":{"begin":0,"end":21}},{"label":"p","span":{"begin":22,"end":779}}],"tracks":[{"project":"2_test","denotations":[{"id":"25557782-19648217-2052276","span":{"begin":448,"end":450},"obj":"19648217"}],"attributes":[{"subj":"25557782-19648217-2052276","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#93ecc3","default":true}]}]}}