InteractionCoefficientGraph

Graphs a scatterplot of pairs vs. the interaction coefficient
for the pair

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

InteractionCoefficientGraph function

<dl><dt>inputResults</dt>
<dd>Data frame with model results (output of ProcessResults())</dd>
<dt>interactionCoeffPercentile</dt>
<dd>percentile cutoff for interaction coefficient 
(default bottom 10 percent (high negative coefficients) and top 10 percent 
(high positive coefficients))</dd>
<dt>percentageToPlot</dt>
<dd>percentage of points to plot (the points will be 
randomly selected) -- plotting all points will likely overwhelm plotting function.</dd>
<dt>independent.var.type</dt>
<dd>type of analyte used as the independent variable 
("1" or "2")</dd>
<dt>outcome</dt>
<dd>type of analyte used as the outcome/dependent variable ("1"
or "2")</dd></dl>

Arguments

Graphs a scatterplot of pairs vs. the interaction coefficient
for the pair — InteractionCoefficientGraph

<dl>

<dt>inputResults</dt>
<dd>Data frame with model results (output of ProcessResults())</dd>


<dt>interactionCoeffPercentile</dt>
<dd>percentile cutoff for interaction coefficient 
(default bottom 10 percent (high negative coefficients) and top 10 percent 
(high positive coefficients))</dd>


<dt>percentageToPlot</dt>
<dd>percentage of points to plot (the points will be 
randomly selected) -- plotting all points will likely overwhelm plotting function.</dd>


<dt>independent.var.type</dt>
<dd>type of analyte used as the independent variable 
("1" or "2")</dd>


<dt>outcome</dt>
<dd>type of analyte used as the outcome/dependent variable ("1"
or "2")</dd>

</dl>

InteractionCoefficientGraph: Graphs a scatterplot of pairs vs. the interaction coefficient for the pair

Description

Usage

Value

Arguments