add_predictors

A helper function to add predictors to a filebacked matrix of data

internal

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

add_predictors function

<dl><dt>obj</dt>
<dd>A <code>bigSNP</code> object</dd>
<dt>add_predictor</dt>
<dd>Optional: add additional covariates/predictors/features from an external file (i.e., not a PLINK file).</dd>
<dt>id_var</dt>
<dd>String specifying which column of the PLINK <code>.fam</code> file has the unique sample identifiers.</dd>
<dt>rds_dir</dt>
<dd>The path to the directory in which you want to create the new <code>.rds</code> and <code>.bk</code> files. Defaults to <code>data_dir</code>(from <code>process_plink()</code> call)</dd>
<dt>outfile</dt>
<dd>A string with the name of the filepath for the log file</dd>
<dt>quiet</dt>
<dd>Logical: should console messages be silenced? Defaults to FALSE</dd></dl>

Arguments

A helper function to add predictors to a filebacked matrix of data — add_predictors

<dl>

<dt>obj</dt>
<dd>A <code>bigSNP</code> object</dd>


<dt>add_predictor</dt>
<dd>Optional: add additional covariates/predictors/features from an external file (i.e., not a PLINK file).</dd>


<dt>id_var</dt>
<dd>String specifying which column of the PLINK <code>.fam</code> file has the unique sample identifiers.</dd>


<dt>rds_dir</dt>
<dd>The path to the directory in which you want to create the new <code>.rds</code> and <code>.bk</code> files. Defaults to <code>data_dir</code>(from <code>process_plink()</code> call)</dd>


<dt>outfile</dt>
<dd>A string with the name of the filepath for the log file</dd>


<dt>quiet</dt>
<dd>Logical: should console messages be silenced? Defaults to FALSE</dd>

</dl>

add_predictors: A helper function to add predictors to a filebacked matrix of data

Description

Usage

Value

Arguments