boot.lucid

This function deprecates. Please use boot_lucid instead.

An implementation of the LUCID model (Peng (2019) <doi:10.1093/bioinformatics/btz667>).
LUCID conducts integrated clustering using exposures, omics data (and outcome
as an option). An EM algorithm is implemented to estimate MLE of the LUCID model.
LUCIDus features integrated variable selection, incorporation of missing omics
data, bootstrap inference, prediction and visualization of the model.

Yinqi Zhao

LUCIDus

Latent Unknown Clustering Integrating Multi-View Data

David Conti

Jesse Goodrich

Cheng Peng

boot.lucid function

<dl><dt>G</dt>
<dd>Exposures, a numeric vector, matrix, or data frame. Categorical variable 
should be transformed into dummy variables. If a matrix or data frame, rows 
represent observations and columns correspond to variables.</dd>
<dt>Z</dt>
<dd>Omics data, a numeric matrix or data frame. Rows correspond to observations
and columns correspond to variables.</dd>
<dt>Y</dt>
<dd>Outcome, a numeric vector. Categorical variable is not allowed. Binary 
outcome should be coded as 0 and 1.</dd>
<dt>CoG</dt>
<dd>Optional, covariates to be adjusted for estimating the latent cluster.
A numeric vector, matrix or data frame. Categorical variable should be transformed 
into dummy variables.</dd>
<dt>CoY</dt>
<dd>Optional, covariates to be adjusted for estimating the association 
between latent cluster and the outcome. A numeric vector, matrix or data frame. 
Categorical variable should be transformed into dummy variables.</dd>
<dt>model</dt>
<dd>A LUCID model fitted by <code>est.lucid</code>.</dd>
<dt>conf</dt>
<dd>A numeric scalar between 0 and 1 to specify confidence level(s) 
of the required interval(s).</dd>
<dt>R</dt>
<dd>An integer to specify number of bootstrap replicates for LUCID model.
If feasible, it is recommended to set R &gt;= 1000.</dd></dl>

Arguments

Deprecated function boot.lucid — boot.lucid

<dl>

<dt>G</dt>
<dd>Exposures, a numeric vector, matrix, or data frame. Categorical variable 
should be transformed into dummy variables. If a matrix or data frame, rows 
represent observations and columns correspond to variables.</dd>


<dt>Z</dt>
<dd>Omics data, a numeric matrix or data frame. Rows correspond to observations
and columns correspond to variables.</dd>


<dt>Y</dt>
<dd>Outcome, a numeric vector. Categorical variable is not allowed. Binary 
outcome should be coded as 0 and 1.</dd>


<dt>CoG</dt>
<dd>Optional, covariates to be adjusted for estimating the latent cluster.
A numeric vector, matrix or data frame. Categorical variable should be transformed 
into dummy variables.</dd>


<dt>CoY</dt>
<dd>Optional, covariates to be adjusted for estimating the association 
between latent cluster and the outcome. A numeric vector, matrix or data frame. 
Categorical variable should be transformed into dummy variables.</dd>


<dt>model</dt>
<dd>A LUCID model fitted by <code>est.lucid</code>.</dd>


<dt>conf</dt>
<dd>A numeric scalar between 0 and 1 to specify confidence level(s) 
of the required interval(s).</dd>


<dt>R</dt>
<dd>An integer to specify number of bootstrap replicates for LUCID model.
If feasible, it is recommended to set R &gt;= 1000.</dd>

</dl>

boot.lucid: Deprecated function boot.lucid

Description

Usage

Arguments