# Single-Iteration Permutation for Large-Scale Biobank Data

## Documentation for package ‘SIP’ version 0.1.0

- DESCRIPTION file
- Package README

## Help Pages

get_fixed | 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_pairPerm | This function samples individuals by pairs for permuting phenotype vectors in the paired-permutation function (sipPair.R)
get_pairPermDF | 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_permDF | This function recombines the fixed data and permuted data into a permuted sample-by-variable data frame.
get_permIdx | 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_permute | This function subsets the sample-by-variable data frame to the permutable data. This subset should include phenotypes and phenotypic covariates.
get_relCat | This function infers relatedness categories in the paired-permutation function (sip_pair.R) prior to permutation.
get_relPairs | This function pairs individuals in the paired-permutation function (sip_pair.R) into the most highly-related pairs possible.
get_sexDF | This function divides the sample-by-variable data frame into males and females prior to permutation within sexes.
get_singSamp | 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).
order_permDF | This function reorders the permuted sample-by-variable data frame to match the ID order of the primary sample-by-variable data frame.
phenotype_IBD_correlation | Phenotype-IBD correlation
plot_phenotype_correlations | Phenotype correlation plot
sip | Single-iteration permutation for large-scale biobank data
sipPair_exampleData | Single-iteration paired permutation phenotype and covariate data
sipPair_relatednessData | Single-iteration paired permutation relatedness data
sip_exampleData | Single-iteration permutation phenotype and covariate data
sip_pair | Single-iteration paired permutation for large-scale biobank data with relatedness