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szhan / tsimpute

Genome-wide genotype imputation using tree sequences.
MIT License
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Compute R-squared between allele dosages of two sets of genotypes #190

Open szhan opened 8 months ago

szhan commented 8 months ago

R-squared between the allele dosage of imputed genotypes and the allele dosage of truth genotypes is a commonly used metric for evaluating the performance of imputation methods. It has been shown that improvements in R-squared can translates to increases in statistical power of GWAS.

szhan commented 6 months ago

Note also that the R-squared statistic is calculated on groups of variants within a MAF bin ("aggregate R2").