standardize_filebacked

A helper function to standardize a filebacked matrix

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

standardize_filebacked function

<dl><dt>X</dt>
<dd>A <code>big.matrix</code> object that has been subset &amp;/or had any additional predictors appended as columns</dd>
<dt>outfile</dt>
<dd>Optional: the name (character string) of the logfile to be written.</dd>
<dt>quiet</dt>
<dd>Logical: should console messages be silenced? Defaults to FALSE</dd>
<dt>tocenter</dt>
<dd>Should the matrix be centered in addition to scaled? Defaults to TRUE.</dd></dl>

Arguments

A helper function to standardize a filebacked matrix — standardize_filebacked

<dl>

<dt>X</dt>
<dd>A <code>big.matrix</code> object that has been subset &amp;/or had any additional predictors appended as columns</dd>


<dt>outfile</dt>
<dd>Optional: the name (character string) of the logfile to be written.</dd>


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


<dt>tocenter</dt>
<dd>Should the matrix be centered in addition to scaled? Defaults to TRUE.</dd>

</dl>

standardize_filebacked: A helper function to standardize a filebacked matrix

Description

Usage

Value

Arguments