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ChemoSpec (version 4.1.15)

Exploratory Chemometrics for Spectroscopy

Description

A collection of functions for top-down exploratory data analysis of spectral data obtained via nuclear magnetic resonance (NMR), infrared (IR) or Raman spectroscopy. Includes functions for plotting and inspecting spectra, peak alignment, hierarchical cluster analysis (HCA), principal components analysis (PCA), model-based clustering and statistical total correlation spectroscopy (STOCSY) analysis. Robust methods appropriate for this type of high-dimensional data are available. ChemoSpec is designed with metabolomics data sets in mind, where the samples fall into groups such as treatment and control. Graphical output is formatted consistently for publication quality plots. ChemoSpec is intended to be very user friendly and help you get usable results quickly. A vignette covering typical operations is available.

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Install

install.packages('ChemoSpec')

Monthly Downloads

957

Version

4.1.15

License

GPL-3

Issues

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Repository

https://github.com/bryanhanson/ChemoSpec

Maintainer

Bryan Hanson

Last Published

July 24th, 2015

Functions in ChemoSpec (4.1.15)

Made Up NMR Data Sets

Normalize a Spectra Object

Average Levels of a Factor in a Data Matrix

Bin or Bucket Data

Plot PCA Loadings from a Spectra Object Against Each Other

Spectra Objects

IR and NMR Spectra of Serenoa repens (Saw Palmetto) Oil Extracts and Reference Oils

Scree Plots of PCA Results for a Spectra Object

Summarize a Spectra Object

Plot PCA Loadings for a Spectra Object

HCA on PCA scores from a Spectra Object

cleanSTOCSYpeaks

Process a List of Cross Peaks

Plot Dendrogram for Spectra Object

Plot a Spectra Object Interactively

Verify the Integrity of a Spectra Object

Remove Frequencies from a Spectra Object

Shrink the Leaves of a Dendrogram Based on a Spectra Object

Plot ANOVA-PCA Scores from a Spectra Object

Conduct Hierarchical Cluster-Based Peak Alignment on a Spectra Object

Conversion Between PCA Classes

Tools for STOCSY Analysis of a Spectra Object

Modified Version of coordProj from mclust

Label Extreme Values in a 2D Data Set

mclust3dSpectra

mclust Analysis of a Spectra Object in 3D

3D PCA Score Plot for a Spectra Object

Interactive 3D Score Plot of a Spectra Object

Determine if a Number is a Whole Number

Compute Distance Between Rows of a Matrix

baselineSpectra

Baseline Correction of a Spectra Object

Read and process a JCAMP-DX file.

Robust PCA of a Spectra Object

Plot aovPCAscores Loadings of a Spectra Object

Check for Missing Values (Gaps)

Change the Color Scheme of a Spectra Object

Plot PCA Scores of a Spectra Object

Colors and Symbols in ChemoSpec and Spectra Objects

Plot HCA Results of a Spectra Object

Remove Samples or Groups from a Spectra Object

Functions to Compute Measures of Central Tendency and Spread. seX!

Compute Confidence Ellipses

Select Levels for Contour and Image Type Plots

Color the Leaves of a Dendrogram Based on a Spectra Object

Create Ellipsoid

s-Plot of Spectra Data Post PCA

ANOVA-PCA Analysis of Spectra Data

Plot Spectra Object

ChemoSpec-package

Exploratory Chemometrics for Spectroscopy

splitSpectraGroups

Create New Groups from an Existing Spectra Object

sampleDistSpectra

Compute the Distance Between Samples in a Spectra Object

Bin or Bucket a Spectra Object

files2SpectraObject

Merge Files in a Directory into a Spectra Object

Evaluate or Compare the Quality of Clusters Quantitatively

mclust Analysis of a Spectra Object PCA Results

labelExtremes3d

Identify Extreme Values in 3D

Sort Rows of a Covariance Matrix of a Spectra Object

Classical PCA of Spectra Objects

Assign Group Membership and Colors for a Spectra Object

mclust Analysis in 3D

plotScoresDecoration

Decorate PCA Score Plot of a Spectra Object

loopThruSpectra

Display the Spectra in a Spectra Object One at a Time

Normalize a Vector to range -1 to +1

Cross-Validation of Classical PCA Results for a Spectra Object

Outlier Diagnostic Plots for PCA of a Spectra Object

Summarize the Group Parameters of a Spectra Object

Plot Measures of Central Tendency and Spread for a Spectra Object

Create a Seriated Heat Map Comparing Samples and Spectral Data for a Spectra Object

Conduct MANOVA using PCA Scores and Factors in a Spectra Object