getLDsets

Extracts marker LD sets based on a sparse LD matrix stored in the Glist object.

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

getLDsets function

<dl><dt>Glist</dt>
<dd>A list structure containing information about genotypes stored on disk.</dd>
<dt>chr</dt>
<dd>A numeric value specifying the chromosome for which LD sets are to be extracted.</dd>
<dt>r2</dt>
<dd>A numeric threshold, defaulting to 0.5, used for extracting LD sets.</dd></dl>

Arguments

Get marker LD sets — getLDsets

<dl>

<dt>Glist</dt>
<dd>A list structure containing information about genotypes stored on disk.</dd>


<dt>chr</dt>
<dd>A numeric value specifying the chromosome for which LD sets are to be extracted.</dd>


<dt>r2</dt>
<dd>A numeric threshold, defaulting to 0.5, used for extracting LD sets.</dd>

</dl>

getLDsets: Get marker LD sets

Description

Usage

Arguments