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For these markers, a MAF of 0.20 was assumed when other SNP within the wave had MAF estimates.
SNPs with a MAF > 0.05 and < 3%% missing data were initially selected.
Simonin et al. (2014) propose a MAF algorithm called c-marking agents.
Figure 5 Results of dimensionality reduction through PCA (a), MAF (b), traditional MNF (c), and OMNF (d).
In our particular case, 21 of the 29 SNPs presented a MAF equal to or higher that 0.3, and only 3 SNPs had a MAF lower than 0.1.
Twenty SNPs were monomorphic or had a MAF of <1% and were excluded from the analysis.
Fifteen haplotype-tagged SNPs (htSNPs) were identified by the HaploBlockFinder software [9] with a MAF ≥5%.
All SNPs having a MAF ≥5% were considered in the association analyses.
In contrast, filtering with a MAF difference of 0.1 or 0.2 retained many false positives.
To overcome this problem, we selected the 394 mtSNPs from the whole dataset fulfilling a MAF >0.05.
a MAF, Minor allele frequency.
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