Single-Iteration Permutation for Large-Scale Biobank Data

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Documentation for package ‘SIP’ version 0.1.0

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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