normalize_global_basic

This function is intended to be used in SPANS only. It is a VERY trimmed down
version of normalize_global. It is trimmed down because within SPANS we only
need the norm_params element from the output of the normalize_global
function. All of the other options and output can be ignored.

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

normalize_global_basic function

<dl><dt>edata</dt>
<dd>a \(p \times n + 1\) data.frame, where \(p\) is the number
of peptides, lipids, or metabolites and \(n\) is the number of samples.
Each row corresponds to data for a peptide, protein, lipid, or metabolite,
with a column giving the identifer name.</dd>
<dt>norm_fn</dt>
<dd>character string indicating the normalization function to use
for normalization. See details for the current offerings.</dd></dl>

Arguments

Normalize e_data within SPANS — normalize_global_basic

<dl>

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


<dt>norm_fn</dt>
<dd>character string indicating the normalization function to use
for normalization. See details for the current offerings.</dd>

</dl>

normalize_global_basic: Normalize e_data within SPANS

Description

Usage

Value

Arguments