set_filter

This function will create a filter class object. The output will always have
the same elements but not all of them will be used for every filter type. This
object will be appended to the list in the filters attribute for an omicsData
object.

internal

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_filter function

<dl><dt>type</dt>
<dd>The type of filter, see <code>filter_objects.R</code></dd>
<dt>threshold</dt>
<dd>The threshold for filtering applied, if applicable.</dd>
<dt>filtered</dt>
<dd>The samples/biomolecules that are filtered.</dd>
<dt>method</dt>
<dd>A list of metadata about what method was used in applying the 
filter.</dd></dl>

Arguments

Sets/updates the filters attribute with a filter class object. — set_filter

<dl>

<dt>type</dt>
<dd>The type of filter, see <code>filter_objects.R</code></dd>


<dt>threshold</dt>
<dd>The threshold for filtering applied, if applicable.</dd>


<dt>filtered</dt>
<dd>The samples/biomolecules that are filtered.</dd>


<dt>method</dt>
<dd>A list of metadata about what method was used in applying the 
filter.</dd>

</dl>

set_filter: Sets/updates the filters attribute with a filter class object.

Description

Usage

Value

Arguments