Selects biomolecules for normalization via the method of percentage of the
peptides (or proteins, metabolites, etc.) present (PPP)

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

ppp function

<dl><dt>e_data</dt>
<dd>a $p \times n + 1$ data.frame, where $p$ is the number
of peptides, proteins, lipids, or metabolites and $n$ is the number of
samples. Each row corresponds to data for a peptide, protein, lipid, or
metabolite, with one column giving the biomolecule identifier name.</dd>
<dt>edata_id</dt>
<dd>character string indicating the name of the peptide, protein,
lipid, or metabolite identifier. Usually obtained by calling
<code>attr(omicsData, "cnames")$edata_cname</code>.</dd>
<dt>proportion</dt>
<dd>numeric value between 0 and 1, indicating the proportion at
or above which a biomolecule must be present across all samples in order to be
retained (default value 0.5)</dd></dl>

Arguments

Author

Identify Biomolecules from the Proportion Present (PPP) for Use in
Normalization — ppp

<dl>

<dt>e_data</dt>
<dd>a $p \times n + 1$ data.frame, where $p$ is the number
of peptides, proteins, lipids, or metabolites and $n$ is the number of
samples. Each row corresponds to data for a peptide, protein, lipid, or
metabolite, with one column giving the biomolecule identifier name.</dd>


<dt>edata_id</dt>
<dd>character string indicating the name of the peptide, protein,
lipid, or metabolite identifier. Usually obtained by calling
<code>attr(omicsData, "cnames")$edata_cname</code>.</dd>


<dt>proportion</dt>
<dd>numeric value between 0 and 1, indicating the proportion at
or above which a biomolecule must be present across all samples in order to be
retained (default value 0.5)</dd>

</dl>

ppp: Identify Biomolecules from the Proportion Present (PPP) for Use in Normalization

Description

Usage

Value

Arguments

Author

Details