fill_data

Impute missing data by optimizing the likelihood function

An implementation of estimating the Latent Unknown Clusters By Integrating Multi-omics Data (LUCID) model (Peng (2019) <doi:10.1093/bioinformatics/btz667>). LUCID conducts integrated clustering using exposures, omics information (and outcome information as an option). This package implements three different integration strategies for multi-omics data analysis within the LUCID framework: LUCID early integration (the original LUCID model), LUCID in parallel (intermediate integration), and LUCID in serial (late integration). Automated model selection for each LUCID model is available to obtain the optimal number of latent clusters, and an integrated imputation approach is implemented to handle sporadic and list-wise missingness in multi-omics data. Lasso-type regularity for exposure and omics features were added. S3 methods for summary and plotting functions were fixed. Fixed minor bugs.

Qiran Jia

LUCIDus

LUCID with Multiple Omics Data

Yinqi Zhao

David Conti

Jesse Goodrich

fill_data function

<dl><dt>obs</dt>
<dd>a vector of length M</dd>
<dt>mu</dt>
<dd>a matrix of size M x K</dd>
<dt>sigma</dt>
<dd>a matrix of size M x M x K</dd>
<dt>p</dt>
<dd>a vector of length K</dd>
<dt>index</dt>
<dd>a vector of length M, indicating whether a value is missing
or not in the raw data</dd>
<dt>lucid_model</dt>
<dd>Specifying LUCID model, "early" for early integration, "parallel" for lucid in parallel,
"serial" for lucid in serial</dd></dl>

Arguments

Impute missing data by optimizing the likelihood function — fill_data

<dl>

<dt>obs</dt>
<dd>a vector of length M</dd>


<dt>mu</dt>
<dd>a matrix of size M x K</dd>


<dt>sigma</dt>
<dd>a matrix of size M x M x K</dd>


<dt>p</dt>
<dd>a vector of length K</dd>


<dt>index</dt>
<dd>a vector of length M, indicating whether a value is missing
or not in the raw data</dd>


<dt>lucid_model</dt>
<dd>Specifying LUCID model, "early" for early integration, "parallel" for lucid in parallel,
"serial" for lucid in serial</dd>

</dl>

fill_data: Impute missing data by optimizing the likelihood function

Description

Usage

Value

Arguments