SIP
Single-Iteration Permutation for Large-Scale Biobank Data
Description
A single, phenome-wide permutation of large-scale biobank data. When a large number of phenotypes are analyzed in parallel, a single permutation across all phenotypes followed by genetic association analyses of the permuted data enables estimation of false discovery rates (FDRs) across the phenome. These FDR estimates provide a significance criterion for interpreting genetic associations in a biobank context. For the basic permutation of unrelated samples, this package takes a sample-by-variable file with ID, genotypic covariates, phenotypic covariates, and phenotypes as input. For data with related samples, it also takes a file with sample pair-wise identity-by-descent information. The function outputs a permuted sample-by-variable file ready for genome-wide association analysis. See Annis et al. (2021) <doi:10.21203/rs.3.rs-873449/v1> for details.
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| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |