admix

A dataset containing the 100 SNPs, a demographic variable representing ancestry,
and a simulated outcome.

datasets

Fits penalized linear mixed models that correct for
unobserved confounding factors. 'plmmr' infers and corrects for the
presence of unobserved confounding effects such as population
stratification and environmental heterogeneity. It then fits a linear
model via penalized maximum likelihood. Originally designed for the
multivariate analysis of single nucleotide polymorphisms (SNPs)
measured in a genome-wide association study (GWAS), 'plmmr' eliminates
the need for subpopulation-specific analyses and post-analysis p-value
adjustments. Functions for the appropriate processing of 'PLINK'
files are also supplied. For examples, see the package homepage
<https://pbreheny.github.io/plmmr/>.

Patrick Breheny

plmmr

Penalized Linear Mixed Models for Correlated Data

Tabitha K. Peter

Anna C. Reisetter

Yujing Lu

Oscar A. Rysavy

Patrick J. Breheny

admix function

A list with 3 components:<dl>
<dt>X</dt>
<dd>SNP matrix (197 observations of 100 SNPs)</dd><dt>y</dt>
<dd>197 x 1 matrix of simulated (continuous) outcomes</dd><dt>ancestry</dt>
<dd>vector with ancestry categorization: 0 = African, 1 = African American, 2 = European, 3 = Japanese</dd>
</dl>

Format

Admix: Semi-simulated SNP data — admix

A list with 3 components:<dl>
<dt>X</dt>
<dd>SNP matrix (197 observations of 100 SNPs)</dd>

<dt>y</dt>
<dd>197 x 1 matrix of simulated (continuous) outcomes</dd>

<dt>ancestry</dt>
<dd>vector with ancestry categorization: 0 = African, 1 = African American, 2 = European, 3 = Japanese</dd>


</dl>

admix: Admix: Semi-simulated SNP data

Description

Usage

Arguments

Format