zrollup

This function applies the zrollup method to a pepData object for each unique
protein and returns a proData object.

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

zrollup function

<dl><dt>pepData</dt>
<dd>an omicsData object of class 'pepData'</dd>
<dt>combine_fn</dt>
<dd>logical indicating what combine_fn to use, defaults to
median, other option is mean</dd>
<dt>parallel</dt>
<dd>logical indicating whether or not to use "doParallel" loop in
applying zrollup function. Defaults to TRUE.</dd></dl>

Arguments

Applies zrollup function — zrollup

<dl>

<dt>pepData</dt>
<dd>an omicsData object of class 'pepData'</dd>


<dt>combine_fn</dt>
<dd>logical indicating what combine_fn to use, defaults to
median, other option is mean</dd>


<dt>parallel</dt>
<dd>logical indicating whether or not to use "doParallel" loop in
applying zrollup function. Defaults to TRUE.</dd>

</dl>

zrollup: Applies zrollup function

Description

Usage

Value

Arguments

Details

References