Package: SIP 0.1.0

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.

Authors:Aubrey Annis [aut, cre]

SIP_0.1.0.tar.gz
SIP_0.1.0.zip(r-4.7)SIP_0.1.0.zip(r-4.6)SIP_0.1.0.zip(r-4.5)
SIP_0.1.0.tgz(r-4.6-any)SIP_0.1.0.tgz(r-4.5-any)
SIP_0.1.0.tar.gz(r-4.7-any)SIP_0.1.0.tar.gz(r-4.6-any)
SIP_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
SIP/json (API)

# Install 'SIP' in R:
install.packages('SIP', repos = c('https://acannis.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/acannis/sip/issues

Datasets:

On CRAN:

Conda:

3.30 score 179 downloads 4 exports 18 dependencies

Last updated from:434de59a11. Checks:7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING128
source / vignettesOK214
linux-release-x86_64WARNING125
macos-release-arm64WARNING81
macos-oldrel-arm64WARNING81
windows-develWARNING72
windows-releaseWARNING66
windows-oldrelWARNING74
wasm-releaseOK105

Exports:phenotype_IBD_correlationplot_phenotype_correlationssipsip_pair

Dependencies:clicpp11data.tablefarverggplot2gluegtableisobandlabelinglifecycleR6RColorBrewerrlangS7scalesvctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
This function subsets the sample-by-variable dataframe to the "fixed" (i.e., non-permuted) data. This subset should include ID variables, sex, and genotypic covariates.get_fixed
This function samples individuals by pairs for permuting phenotype vectors in the paired-permutation function (sipPair.R)get_pairPerm
This function recombines the fixed data and permuted data in the paired-permutation function (sipPair.R) into a permuted sample-by-variable data frame.get_pairPermDF
This function recombines the fixed data and permuted data into a permuted sample-by-variable data frame.get_permDF
This function samples indices for permuting phenotype vectors in the basic permutation function (sip.R) and for permuting leftover unpaired individuals in the paired-permutation function (sipPair.R).get_permIdx
This function subsets the sample-by-variable data frame to the permutable data. This subset should include phenotypes and phenotypic covariates.get_permute
This function infers relatedness categories in the paired-permutation function (sip_pair.R) prior to permutation.get_relCat
This function pairs individuals in the paired-permutation function (sip_pair.R) into the most highly-related pairs possible.get_relPairs
This function divides the sample-by-variable data frame into males and females prior to permutation within sexes.get_sexDF
This function checks for uneven numbers of individuals within relatedness category and creates a data set for permuting single samples that will not be pair permuted (sip_pair.R).get_singSamp
This function reorders the permuted sample-by-variable data frame to match the ID order of the primary sample-by-variable data frame.order_permDF
Phenotype-IBD correlationphenotype_IBD_correlation
Phenotype correlation plotplot_phenotype_correlations
Single-iteration permutation for large-scale biobank datasip
Single-iteration permutation phenotype and covariate datasip_exampleData
Single-iteration paired permutation for large-scale biobank data with relatednesssip_pair
Single-iteration paired permutation phenotype and covariate datasipPair_exampleData
Single-iteration paired permutation relatedness datasipPair_relatednessData