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gcxgclab (version 1.0.1)

GCxGC Preprocessing and Analysis

Description

Provides complete detailed preprocessing of two-dimensional gas chromatogram (GCxGC) samples. Baseline correction, smoothing, peak detection, and peak alignment. Also provided are some analysis functions, such as finding extracted ion chromatograms, finding mass spectral data, targeted analysis, and nontargeted analysis with either the 'National Institute of Standards and Technology Mass Spectral Library' or with the mass data. There are also several visualization methods provided for each step of the preprocessing and analysis.

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Version

Install

install.packages('gcxgclab')

Monthly Downloads

129

Version

1.0.1

License

GPL (>= 3)

Maintainer

Stephanie Gamble

Last Published

January 22nd, 2024

Functions in gcxgclab (1.0.1)

non_targeted

Compares MS to atomic mass data
plot_chr

Plot chromatogram
batch_preprocess

Batch reprocessing
gauss

1D Gaussian function
gauss2

2D Gaussian function
plot_peakonly

Plot only peaks
preprocess

Preprocessing
plot_defect

Plots the Kendrick Mass Defect of a peak
mass_list

Creates list of atomic mass data
gauss2_fit

Fitting to 2D Gaussian curve
gauss_fit

Fitting to Gaussian curve
phase_shift

Phase shift
nist_list

Creates list of NIST data
thr_peaks

Threshold Peaks
plot_gauss

Plots a peak with the fitted Gaussian curve.
plot_eic

Plots the EICs
top_peaks

Top Peaks
plot_nist

Plots the mass spectra of a NIST compound.
smooth

Smoothing
targeted

Targeted Analysis
plot_peak

Peak Plot
plot_gauss2

Plots a 3D peak with the fitted Gaussian curve.
plot_ms

Plots the mass spectra of a peak.
comp_nist

Compares MS to NIST MS database
batch_ms

Finds batch of mass spectra
find_eic

Finds EICs
align

Reference Batch Align
comp_peaks

Compare Peaks
bl_corr

Baseline correction
extract_data

Extracts data from cdf file.
batch_eic

Finds batch of EICs
find_ms

Finds MS