We focused on properties that measure variant representation, base quality, and sequence and mapping contexts.
Let ∑ u,m be the correlation matrix between the unmeasured and measured variants and ∑ m,m be the correlation matrix among the measured variants, which are both estimated from a reference panel.
If we define D as the set of IBD = 2 loci among the measured variants and N as the set of IBD ≠ 2 loci, then N + D = G is the total number of measured variants and (2) and (3) Letting w = [ N D] be the probability vector for being in state IBD = 2 or IBD ≠ 2, we have w = wT.
This example shows the potential gain in power attained by using many genetic variants from a single gene region.> -wrap-foot> Estimands and 95%% credible intervals are estimated from Bayesian likelihood-based method using all 17 measured variants, using the 6 variants associated with calcium in the EPIC-InterAct dataset (p < 0.1), and using the lead variant (rs1801725) only.
Presentations of results from GWA studies often report the summary associations of all variants that have reached a certain P-value threshold, and recently the release of association estimates in published GWA studies for all measured variants has been advocated [Editorial, 2012].
and F1 measures, the standard variant, minimum (Min) and maximum (Max) values of accuracy, precision, recall and F1 measures.
Association is assumed to arise because the function of the gene has been altered in some way by the measured variant - or another in linkage disequilibrium with it - and that the change in gene function influences the phenotype.
Both aCGH and paired-end mapping do not precisely identify the boundaries, or breakpoints, of the measured variant.
To account for the selected case sampling (ascertainment), a statistical model that assumes that the effect of any measured variant multiplies the effect of unmeasured variants was applied.
The sequencing results of the two technical replicates (samples 768_1L and 768_2L) were used to analyze different enrichment measures, variant detection rates, and the reproducibility of the method.
