adjLDStat

Check concordance between predicted and observed marker effect. Marker effect is predicted based on sparse LD matrix 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

adjLDStat function

<dl><dt>stat</dt>
<dd>data frame with marker summary statistics (see required format above)</dd>
<dt>Glist</dt>
<dd>list of information about genotype matrix stored on disk</dd>
<dt>chr</dt>
<dd>chromosome for which marker effect is checked</dd>
<dt>region</dt>
<dd>genome region (in base pairs) for which marker effect is checked</dd>
<dt>msize</dt>
<dd>is the number of markers used in the prediction</dd>
<dt>threshold</dt>
<dd>p-value threshold used for chisquare test for difference between observed and predicted marker effects</dd>
<dt>overlap</dt>
<dd>is the number of markers overlapping between adjacent genome region</dd>
<dt>niter</dt>
<dd>is the number of iteration used for detecting outliers</dd></dl>

Arguments

Check concordance between marker effect and sparse LD matrix. — adjLDStat

<dl>

<dt>stat</dt>
<dd>data frame with marker summary statistics (see required format above)</dd>


<dt>Glist</dt>
<dd>list of information about genotype matrix stored on disk</dd>


<dt>chr</dt>
<dd>chromosome for which marker effect is checked</dd>


<dt>region</dt>
<dd>genome region (in base pairs) for which marker effect is checked</dd>


<dt>msize</dt>
<dd>is the number of markers used in the prediction</dd>


<dt>threshold</dt>
<dd>p-value threshold used for chisquare test for difference between observed and predicted marker effects</dd>


<dt>overlap</dt>
<dd>is the number of markers overlapping between adjacent genome region</dd>


<dt>niter</dt>
<dd>is the number of iteration used for detecting outliers</dd>

</dl>

adjLDStat: Check concordance between marker effect and sparse LD matrix.

Description

Usage

Arguments