IntLimData-class

This workflow takes analyte levels from two different types of analytes (e.g. gene expression and metabolite abundance), meta-information on each analyte type, and sample outcome and metadata to identify analyte pairs that are significantly associated with a continuous or discrete outcome (e.g. drug response or tumor type). The following references describe the methods in this package: (1) Jalal K. Siddiqui, et al. (2018) <doi:10.1186/s12859-018-2085-6>, (2) Andrew Patt, et al. (2019) <doi:10.1007/978-1-4939-9027-6_23>.

Tara Eicher

IntLIM

Integration of Omics Data Using Linear Modeling

Jalal Siddiqui

Shunchao Wang

Rohith Vanam

Elizabeth Baskin

Kyle Spencer

Ewy Mathe

IntLimData-class function

<dl>
<dt><code>analyteType1</code></dt>
<dd>A matrix of abundance, expression, or other levels for
a specific type of analyte (e.g. protein abundance, metabolite abundance, or
gene expression)</dd></dl>
<dt><code>analyteType2</code></dt>
<dd>A second matrix of abundance, expression, or other levels for
a specific type of analyte (e.g. protein abundance, metabolite abundance, or
gene expression)</dd>
<dt><code>analyteType1MetaData</code></dt>
<dd>A data frame of metadata for analyte type 1.</dd>
<dt><code>analyteType2MetaData</code></dt>
<dd>A data frame of metadata for analyte type 2.</dd>
<dt><code>sampleMetaData</code></dt>
<dd>A data frame of covariate values from the patient data.</dd>

Slots

IntLimData class — IntLimData-class

<dl>
<dt><code>analyteType1</code></dt>
<dd>A matrix of abundance, expression, or other levels for
a specific type of analyte (e.g. protein abundance, metabolite abundance, or
gene expression)</dd>


<dt><code>analyteType2</code></dt>
<dd>A second matrix of abundance, expression, or other levels for
a specific type of analyte (e.g. protein abundance, metabolite abundance, or
gene expression)</dd>


<dt><code>analyteType1MetaData</code></dt>
<dd>A data frame of metadata for analyte type 1.</dd>


<dt><code>analyteType2MetaData</code></dt>
<dd>A data frame of metadata for analyte type 2.</dd>


<dt><code>sampleMetaData</code></dt>
<dd>A data frame of covariate values from the patient data.</dd>


</dl>

IntLimData class

IntLimData-class: IntLimData class

Description

Arguments

Slots