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SIP  

Single-Iteration Permutation for Large-Scale Biobank Data
View on CRAN: Click here


Download and install SIP package within the R console
Install from CRAN:
install.packages("SIP")

Install from Github:
library("remotes")
install_github("cran/SIP")

Install by package version:
library("remotes")
install_version("SIP", "0.1.0")



Attach the package and use:
library("SIP")
Maintained by
Aubrey Annis
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2025-12-09
Latest Update: 2025-12-09
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.
How to cite:
Aubrey Annis (2025). SIP: Single-Iteration Permutation for Large-Scale Biobank Data. R package version 0.1.0, https://cran.r-project.org/web/packages/SIP. Accessed 04 Jul. 2026.
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