averageReplicates

Average the replicates in a <code>Spectra</code> object and return a new Spectra object
with fewer samples. One should probably not do this until each individual sample has been
visualized for quality control, in case it is a potential outlier.

utilities

A collection of functions for top-down exploratory data analysis
of spectral data including nuclear magnetic resonance (NMR), infrared (IR),
Raman, X-ray fluorescence (XRF) and other similar types of spectroscopy.
Includes functions for plotting and inspecting spectra, peak alignment,
hierarchical cluster analysis (HCA), principal components analysis (PCA) and
model-based clustering. Robust methods appropriate for this type of
high-dimensional data are available. ChemoSpec is designed for structured
experiments, such as metabolomics investigations, where the samples fall into
treatment and control groups. Graphical output is formatted consistently for
publication quality plots. ChemoSpec is intended to be very user friendly and
to help you get usable results quickly. A vignette covering typical operations
is available.

Bryan Hanson

ChemoSpec

Exploratory Chemometrics for Spectroscopy

Bryan A. Hanson

Mike Bostock

Matt Keinsley

Tejasvi Gupta

averageReplicates function

<dl><dt>spectra</dt>
<dd>An object of S3 class <code>Spectra()</code>.</dd>
<dt>uniq</dt>
<dd>Character. A character vector containing strings representing unique sample
identifiers. The sample names will be searched for these strings, and all samples
matching a given string will be averaged and put into a new Spectra object. For
example, consider the case where samples are named
<code>S_1_01, S_1_02, ..., S_2_01, S_2_02, ...</code>
where <code>_01</code> and so forth signifies replicates of a particular sample.
With <code>uniq = c("S_1", "S_2")</code> all <code>S_1</code> replicates will be averaged and
all <code>S_2</code> replicates will be averaged. N.B. the strings will be used as
regex pattern and grepped.</dd></dl>

Arguments

Bryan A. Hanson (DePauw University).

Author

Average Replicates in a Spectra Object — averageReplicates

<dl>

<dt>spectra</dt>
<dd>An object of S3 class <code>Spectra()</code>.</dd>


<dt>uniq</dt>
<dd>Character. A character vector containing strings representing unique sample
identifiers. The sample names will be searched for these strings, and all samples
matching a given string will be averaged and put into a new Spectra object. For
example, consider the case where samples are named
<code>S_1_01, S_1_02, ..., S_2_01, S_2_02, ...</code>
where <code>_01</code> and so forth signifies replicates of a particular sample.
With <code>uniq = c("S_1", "S_2")</code> all <code>S_1</code> replicates will be averaged and
all <code>S_2</code> replicates will be averaged. N.B. the strings will be used as
regex pattern and grepped.</dd>

</dl>

averageReplicates: Average Replicates in a Spectra Object

Description

Usage

Value

Arguments

Author

Examples