adjustB

This function adjusts the B-values based on the LD structure and other parameters.
The adjustment is done in subsets, and a plot of observed vs. predicted values is produced for each subset.

internal

Provides an infrastructure for efficient processing of large-scale genetic and phenotypic data including core functions for: 1) fitting linear mixed models, 2) constructing marker-based genomic relationship matrices, 3) estimating genetic parameters (heritability and correlation), 4) performing genomic prediction and genetic risk profiling, and 5) single or multi-marker association analyses.
Rohde et al. (2019) <doi:10.1101/503631>.

Peter Soerensen

Statistical Tools for Quantitative Genetic Analyses

Palle Duun Rohde

Izel Fourie Soerensen

adjustB function

<dl><dt>b</dt>
<dd>A numeric vector containing the B-values to be adjusted. If NULL (default), no adjustments are made.</dd>
<dt>LD</dt>
<dd>A matrix representing the linkage disequilibrium (LD) structure.</dd>
<dt>msize</dt>
<dd>An integer specifying the size of the subsets.</dd>
<dt>overlap</dt>
<dd>An integer specifying the overlap size between consecutive subsets.</dd>
<dt>shrink</dt>
<dd>A numeric value used for shrinkage. Default is 0.001.</dd>
<dt>threshold</dt>
<dd>A numeric value specifying the threshold. Default is 1e-8.</dd></dl>

Arguments

Adjust B-values — adjustB

<dl>

<dt>b</dt>
<dd>A numeric vector containing the B-values to be adjusted. If NULL (default), no adjustments are made.</dd>


<dt>LD</dt>
<dd>A matrix representing the linkage disequilibrium (LD) structure.</dd>


<dt>msize</dt>
<dd>An integer specifying the size of the subsets.</dd>


<dt>overlap</dt>
<dd>An integer specifying the overlap size between consecutive subsets.</dd>


<dt>shrink</dt>
<dd>A numeric value used for shrinkage. Default is 0.001.</dd>


<dt>threshold</dt>
<dd>A numeric value specifying the threshold. Default is 1e-8.</dd>

</dl>

adjustB: Adjust B-values

Description

Usage

Value

Arguments