pquant

This function takes in a pepData object 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

pquant function

<dl><dt>pepData</dt>
<dd>omicsData object of class 'pepData'</dd>
<dt>combine_fn</dt>
<dd>A character string that can either be 'mean', 'median', 
sum', or a function (e.g., combine_fn_mean, combine_fn_median, combine_fn_sum)</dd></dl>

Arguments

Protein Quantitation using Mean or Median Peptide Abundances — pquant

<dl>

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


<dt>combine_fn</dt>
<dd>A character string that can either be 'mean', 'median', 
sum', or a function (e.g., combine_fn_mean, combine_fn_median, combine_fn_sum)</dd>

</dl>

pquant: Protein Quantitation using Mean or Median Peptide Abundances

Description

Usage

Value

Arguments