getLD

Extracts and returns a sparse LD (Linkage Disequilibrium) matrix for the specified chromosome based on genotypic data provided in `Glist`.

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

getLD function

<dl><dt>Glist</dt>
<dd>A list structure containing genotypic data, including rsids for LD calculation (`rsidsLD`), LD file locations (`ldfiles`), and `msize` which indicates the size for surrounding region to consider for LD.</dd>
<dt>chr</dt>
<dd>A specific chromosome from which LD sets need to be extracted.</dd>
<dt>rsids</dt>
<dd>A vector of rsids that need to be included in the sparse LD matrix. Default is NULL, implying all rsids in the chromosome will be used.</dd></dl>

Arguments

Retrieve Sparse LD Matrix for a Given Chromosome — getLD

<dl>

<dt>Glist</dt>
<dd>A list structure containing genotypic data, including rsids for LD calculation (`rsidsLD`), LD file locations (`ldfiles`), and `msize` which indicates the size for surrounding region to consider for LD.</dd>


<dt>chr</dt>
<dd>A specific chromosome from which LD sets need to be extracted.</dd>


<dt>rsids</dt>
<dd>A vector of rsids that need to be included in the sparse LD matrix. Default is NULL, implying all rsids in the chromosome will be used.</dd>

</dl>

getLD: Retrieve Sparse LD Matrix for a Given Chromosome

Description

Usage

Value

Arguments

Details