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QTL analysis was performed by single marker regression analysis (Kearsey and Hyne [1994]) with Qgene 4.3 (Joehanes and Nelson [2008]).
Furthermore, a combined cross analysis based on 12 common markers in the G8 and G10 cohorts resulted in strengthened evidence for linkage to neurodegeneration for Vra1, as the LOD score rose to 5.9 using marker regression analysis (Fig 2A).
We used marker regression analysis to estimate the allelic effect sizes of the mapped QTLs.
A weighted marker regression analysis was used within this program to calculate likelihood ratio statistic (LRS) scores for each marker.
To evaluate the predictability of E. coli by the BacR marker, regression analysis of these parameters was performed for the HFM and the EVENT data sets.
The SNP that had a p-value from the permutation test of less than 0.10 for the single marker regression analysis were used as predictor variable in order to reduce computational time.
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The five SSR markers detected previously by single-marker regression analysis were within this QTL region.
The LD decay method is possibly the best across all scenarios, but the two-marker regression analysis is almost as good.
The test of association between a marker and QTL and the power of the test were calculated based on single-marker regression analysis.
We present results for the single-marker regression analysis, ridge regression, lasso, GcFlasso, GwFlasso and GwFlasso in Figure 9C H, respectively, where the rows represent phenotypes, and the columns correspond to genotypes, with bright pixels indicating high strength of association.
As shown in Figures 9C and E, both the single-marker regression analysis and lasso find a SNP near the top row, known as Q551R, as significantly associated with a block of correlated phenotypes.
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