Istep_Z

Impute missing data in Z by maximizing the likelihood given fixed
parameters of LUCID

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

Istep_Z function

<dl><dt>Z</dt>
<dd>an N by P matrix representing the omics data</dd>
<dt>p</dt>
<dd>an N by K matrix representing inclusion probability for each
latent cluster</dd>
<dt>mu</dt>
<dd>an M by K matrix representing cluster-specific means</dd>
<dt>sigma</dt>
<dd>an M by M by K array representing cluster-specific covariance</dd>
<dt>index</dt>
<dd>an N by M matrix representing missing values in Z</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

I-step of LUCID — Istep_Z

<dl>

<dt>Z</dt>
<dd>an N by P matrix representing the omics data</dd>


<dt>p</dt>
<dd>an N by K matrix representing inclusion probability for each
latent cluster</dd>


<dt>mu</dt>
<dd>an M by K matrix representing cluster-specific means</dd>


<dt>sigma</dt>
<dd>an M by M by K array representing cluster-specific covariance</dd>


<dt>index</dt>
<dd>an N by M matrix representing missing values in Z</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>

Istep_Z: I-step of LUCID

Description

Usage

Value

Arguments