Local ancestry information has been used to identify genetic susceptibility loci.Results: In this study, we developed a statistical method, efficient inference of local ancestry (EILA), which uses fused quantile regression and k-means classifier to infer the local ancestry for admixed individuals. ...
k-mer counts suggest that the sample probably carries the alleles of the green and blue haplotypes. The second bubble is poorly covered byk-mers; however, linkage to adjacent bubbles can be used to infer the two local haplotype paths.
We also compared the performance of HEELS with that of HESS, which is a state-of-the-art method for local heritability estimation12. We found that the HESS estimator is sensitive to the degree of LD regularization applied through the truncated SVD (Supplementary Fig. 2), a phenomenon that ha...
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Kidd, Progress toward an efficient panel of SNPs for ancestry inference, Forensic Sci. Int. Genet. 10 (2014) 23-32.Kidd KK, Speed WC, Pakstis AJ, Furtado MR, Fang R, Madbouly A, et al. Progress toward an efficient panel of SNPs for ancestry inference. Forensic Sci. Int. Genet. ...
Next, we contribute a novel method for imputation-based local ancestry inference that effectively exploits Linkage Disequilibrium (LD) information. Experiments on simulated admixed populations show that imputation-based ancestry inference has significantly better accuracy over the best current methods for ...
(k\)for inference, we tested values of\(k\)ranging from 5 to 50 and found that median F1 remained highly stable (0.82–0.84) across choices of\(k\)(Supplementary Fig.8d). To evaluate query trajectory inference, we used the Symphony joint embedding to position query cells from the MEM ...
(Supplementary Fig.S2). Although it is very difficult to accurately assign an accession to a geographical region at district level resolution, genotypic similarities and ancestry relationships can be used to group them together with other accession that have the metadata available. We used such ...