adjustMapLD

Adjusts the linkage disequilibrium (LD) values based on map information, effective population size,
and sample size used for map construction.

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

adjustMapLD function

<dl><dt>LD</dt>
<dd>A matrix representing the linkage disequilibrium (LD) structure.</dd>
<dt>map</dt>
<dd>A numeric vector containing the map information.</dd>
<dt>neff</dt>
<dd>An integer representing the effective population size. Default is 11600.</dd>
<dt>nmap</dt>
<dd>An integer representing the sample size used for map construction. Default is 186.</dd>
<dt>threshold</dt>
<dd>A numeric value specifying the threshold for setting LD to zero. Currently unused in the function. Default is 0.001.</dd></dl>

Arguments

Adjust Linkage Disequilibrium (LD) Using Map Information — adjustMapLD

<dl>

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


<dt>map</dt>
<dd>A numeric vector containing the map information.</dd>


<dt>neff</dt>
<dd>An integer representing the effective population size. Default is 11600.</dd>


<dt>nmap</dt>
<dd>An integer representing the sample size used for map construction. Default is 186.</dd>


<dt>threshold</dt>
<dd>A numeric value specifying the threshold for setting LD to zero. Currently unused in the function. Default is 0.001.</dd>

</dl>

adjustMapLD: Adjust Linkage Disequilibrium (LD) Using Map Information

Description

Usage

Value

Arguments