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.

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.

Aubrey Annis

Single-Iteration Permutation for Large-Scale Biobank Data

get_fixed function

<dl><dt>df</dt>
<dd>Data frame</dd>
<dt>id.var, sex.var</dt>
<dd>String</dd>
<dt>geno.vars</dt>
<dd>Character vector</dd></dl>

Arguments

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

<dl>

<dt>df</dt>
<dd>Data frame</dd>


<dt>id.var, sex.var</dt>
<dd>String</dd>


<dt>geno.vars</dt>
<dd>Character vector</dd>

</dl>

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 subsets the sample-by-variable dataframe to the "fixed" (i.e., non-permuted) data. This subset should include ID variables, sex, and genotypic covariates.

Description

Usage

Value

Arguments