Sentence examples for proper info from inspiring English sources

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SNPs with low minor allele frequency (<1%), low imputation quality (MACH: Rsq < 0.3; or IMPUTE: proper info < 0.4) were removed.

The Imputed SNPs with high genotype information content (proper info > 0.5 for IMPUTE and Rsq > 0.3 for MACH) were retained for the further association analysis.

Imputed SNPs were filtered out if they had an MAF < 0.05 or proper info <0.5, allowing for us to test a further 1 709 209 SNPs for association.

Specifically, we used a cut-off of rsq_hat < 0.3 for genotypes imputed with MACH (20), BEAGLE (21) and PLINK (22) software and a cut-off of proper info score <0.5 for IMPUTE (23) software.

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As the QC measure, SNPTEST produces a "proper-info" to measure the relative statistical information about the parameters of interest.

The SNPTEST freq-add-proper-info score has been shown to be highly correlated with the IMPUTE-info score under the additive model.

Imputation results were filtered by minor allele frequency (MAF) of the markers (SNPs with MAFs<5% were excluded, since the procedure generates genotypes for a high number of rare variants that could give spurious association results), by missing data proportion (set to a 5% max), and the frequentist-add-proper-info column of the output.

On the basis of these results, we chose to use the IMPUTE-info score with a filtering threshold <0.8 and MAF <5%, which effectively eliminated ∼79% of the significant SNPs while retaining ∼85% of the nonsignificant ones (SNPTEST freq-add-proper-info <0.9 and MAF 5% would be roughly equivalent to this eliminating ∼73% of the significant SNPs while retaining ∼89% of the nonsignificant ones).

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