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: 7.3.3
Suggests: testthat (>= 3.0.0)
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2025-12-02 14:26:37 UTC; mk
Author: Aubrey Annis [aut, cre]
Maintainer: Aubrey Annis <acannis@umich.edu>
Repository: CRAN
Date/Publication: 2025-12-09 08:00:02 UTC
Built: R 4.6.0; ; 2026-04-28 11:07:05 UTC; unix
