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LDpred2: Test LDSC regression result #154

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deepchocolate opened this issue Apr 19, 2023 · 1 comment
Open

LDpred2: Test LDSC regression result #154

deepchocolate opened this issue Apr 19, 2023 · 1 comment
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@deepchocolate
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deepchocolate commented Apr 19, 2023

Is your feature request related to a problem? Please describe.
One important step in ldpred2 is the LD-score regression. Currently, the output of this is not tested.

cat('\n### Running LD score regression\n')
ldsc <- with(df_beta, snp_ldsc(ld, ld_size, chi2=(beta/beta_se)^2, sample_size=n_eff, blocks=NULL))
h2_est <- ldsc[["h2"]]
cat('Results:', 'Intercept =', ldsc[["int"]], 'H2 =', h2_est, '\n')

Describe the solution you'd like
Reorganize ldpred2.R so that this step is easy to test by moving code into the fun.R script so that it can be run separately. It's probably best to add this as part of testing the results of the tutorial in usecases/LDpred2_test/unittests/tutorial.R. Might aswell add a command-line interface to bigsnpr::snp_ldsc while at it.

Describe alternatives you've considered
None

Additional context
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@deepchocolate deepchocolate self-assigned this Apr 19, 2023
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This issue appears to be stale due to non-activity

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