SIP: Single-Iteration Permutation for Large-Scale Biobank Data

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 (may not be active yet)
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

Documentation:

Reference manual:

SIP.html , SIP.pdf

Downloads:

Package source:	SIP_0.1.0.tar.gz
Windows binaries:	r-devel: not available, r-release: not available, r-oldrel: not available
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

Linking:

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