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.
| Version: | 0.1.0 |
| Depends: | R (≥ 3.5) |
| Imports: | stats, data.table, ggplot2 |
| Suggests: | testthat (≥ 3.0.0) |
| Published: | 2025-12-09 |
| DOI: | 10.32614/CRAN.package.SIP |
| Author: | Aubrey Annis [aut, cre] |
| Maintainer: | Aubrey Annis <acannis at umich.edu> |
| BugReports: | https://github.com/acannis/SIP/issues |
| License: | MIT + file LICENSE |
| URL: | https://github.com/acannis/SIP |
| NeedsCompilation: | no |
| Materials: | README |
| CRAN checks: | SIP results |
| Reference manual: | SIP.html , SIP.pdf |
| Package source: | SIP_0.1.0.tar.gz |
| Windows binaries: | r-devel: SIP_0.1.0.zip, r-release: SIP_0.1.0.zip, r-oldrel: SIP_0.1.0.zip |
| macOS binaries: | r-release (arm64): SIP_0.1.0.tgz, r-oldrel (arm64): SIP_0.1.0.tgz, r-release (x86_64): SIP_0.1.0.tgz, r-oldrel (x86_64): SIP_0.1.0.tgz |
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