An LdEigen reference for the eigendecomposition-based
heritability estimators (estimateH2 with
method = "lder" or "hdl", and
computeLdScores). Built by buildLdEigen
over the first 14 chr22 LD blocks of the de-identified
protocol_example reference. Describes the same variants as
ldScoreExample, so the four estimators can be compared on
one reference.
The LD is that of a panel of 20,000 people simulated from the
protocol_example panel's own LD, which is a sketch of 60 people:
the estimators correct for the noise in a reference's LD, and at 60 that
correction swamps the signal. A large simulated panel keeps the LD
structure real while giving the reference a realistic size
(nSamples = 20000); see inst/scripts/build_h2_examples.R.
Format
An LdEigen object (extends LdStatistic) with an
eigenList of per-block values / vectors /
snpIdx over 1300 variants in 14 LD blocks.
Examples
data(ldEigenExample)
ldEigenExample
#> LdEigen: 1300 SNPs across 14 blocks
#> Eigenvalue truncation: 1.00
#> Reference N: 20000, In-sample: FALSE