Package: SIP
Type: Package
Title: Single-Iteration Permutation for Large-Scale Biobank Data
Version: 0.1.0
Authors@R: c(person("Aubrey", "Annis", role = c("aut", "cre"), email = "acannis@umich.edu"))
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.
URL: https://github.com/acannis/SIP
BugReports: https://github.com/acannis/SIP/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5)
Imports: stats, data.table, ggplot2
RoxygenNote: 7.3.2
Suggests: testthat (>= 3.0.0)
Config/testthat/edition: 3
Repository: https://acannis.r-universe.dev
Date/Publication: 2026-06-26 21:52:24 UTC
RemoteUrl: https://github.com/acannis/sip
RemoteRef: HEAD
RemoteSha: 434de59a11d602d83f1394b492fa7dd8926e3833
NeedsCompilation: no
Packaged: 2026-06-26 22:14:08 UTC; root
Author: Aubrey Annis [aut, cre]
Maintainer: Aubrey Annis <acannis@umich.edu>