set_check_names

This function sets the check.names attribute of an omicsData object.
This function has been deprecated in favor of handling checking names
externally and will return an unmodified omicsData.

Provides functionality for quality control processing and statistical analysis of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level), lipidomic, and metabolomic data, as well as RNA-seq based count data and nuclear magnetic resonance (NMR) data. This includes data transformation, specification of groups that are to be compared against each other, filtering of features and/or samples, data normalization, data summarization (correlation, PCA), and statistical comparisons between defined groups. Implements methods described in: Webb-Robertson et al. (2014) <doi:10.1074/mcp.M113.030932>. Webb-Robertson et al. (2011) <doi:10.1002/pmic.201100078>. Matzke et al. (2011) <doi:10.1093/bioinformatics/btr479>. Matzke et al. (2013) <doi:10.1002/pmic.201200269>. Polpitiya et al. (2008) <doi:10.1093/bioinformatics/btn217>. Webb-Robertson et al. (2010) <doi:10.1021/pr1005247>.

Lisa Bramer

pmartR

Panomics Marketplace - Quality Control and Statistical Analysis
for Panomics Data

Kelly Stratton

Daniel Claborne

Evan Glasscock

Rachel Richardson

David Degnan

Evan Martin

set_check_names function

<dl><dt>omicsData</dt>
<dd>an object of the class 'pepData', 'proData', 'metabData',
'lipidData', or 'nmrData', usually created by <code>as.pepData</code>,
<code>as.proData</code>, <code>as.metabData</code>,
<code>as.lipidData</code>, or <code>as.nmrData</code>, respectively.</dd>
<dt>set_to</dt>
<dd>logical indicating what to set check.names attribute to.
Defaults to TRUE.</dd></dl>

Arguments

DEPRECATED: Set check.names attribute of omicsData object — set_check_names

<dl>

<dt>omicsData</dt>
<dd>an object of the class 'pepData', 'proData', 'metabData',
'lipidData', or 'nmrData', usually created by <code>as.pepData</code>,
<code>as.proData</code>, <code>as.metabData</code>,
<code>as.lipidData</code>, or <code>as.nmrData</code>, respectively.</dd>


<dt>set_to</dt>
<dd>logical indicating what to set check.names attribute to.
Defaults to TRUE.</dd>

</dl>

set_check_names: DEPRECATED: Set check.names attribute of omicsData object

Description

Usage

Value

Arguments