pvalCoefVolcano

'volcano' plot (difference in correlations vs p-values)
of all pairs

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

pvalCoefVolcano function

<dl><dt>inputResults</dt>
<dd>Data frame with model results (output of ProcessResults())</dd>
<dt>inputData</dt>
<dd>Named list (output of 
FilterData()) with analyte levels 
and associated meta-data</dd>
<dt>nrpoints</dt>
<dd>number of points to be plotted in lowest density areas (see 'smoothScatter' documentation for more detail)</dd>
<dt>pvalcutoff</dt>
<dd>cutoff of FDR-adjusted p-value for filtering (default 0.05)</dd>
<dt>coefPercentileCutoff</dt>
<dd>cutoff of interaction coefficient percentile.</dd></dl>

Arguments

'volcano' plot (difference in correlations vs p-values)
of all pairs — pvalCoefVolcano

<dl>

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


<dt>inputData</dt>
<dd>Named list (output of 
FilterData()) with analyte levels 
and associated meta-data</dd>


<dt>nrpoints</dt>
<dd>number of points to be plotted in lowest density areas (see 'smoothScatter' documentation for more detail)</dd>


<dt>pvalcutoff</dt>
<dd>cutoff of FDR-adjusted p-value for filtering (default 0.05)</dd>


<dt>coefPercentileCutoff</dt>
<dd>cutoff of interaction coefficient percentile.</dd>

</dl>

pvalCoefVolcano: 'volcano' plot (difference in correlations vs p-values) of all pairs

Description

Usage

Value

Arguments