A framework for deconvolution, alignment and postprocessing of 1D NMR spectra, resulting in a data matrix of aligned signal integrals. The deconvolution part uses the algorithm described in Koh et al. (2009). The alignment part is based on functions from the ‘speaq’ package, described in Beirnaert et al. (2018) and Vu et al. (2011). A detailed description and evaluation of an early version of the package, ‘MetaboDecon1D v0.2.2’, can be found in Haeckl et al. (2021).
Installation
To install the stable version from CRAN, including all Bioconductor dependencies, paste the following commands in a running R session (e.g. in RStudio):
install.packages("pak")
pak::pkg_install("metabodecon")Alternatively, if you prefer installing via the traditional install.packages() function, you can do so by running the following commands:
# Install Bioconductor dependencies
install.packages("BiocManager")
BiocManager::install(c("MassSpecWavelet", "impute"))
# Install metabodecon
install.packages("metabodecon")To install the development version from GitHub use:
install.packages("pak")
pak::pkg_install("spang-lab/metabodecon")Usage
At Get Started you can see an example how metabodecon can be used to deconvolute an existing data set, followed by alignment of the data and some additional postprocessing steps, resulting in a data matrix of aligned signal integrals.
At Function Reference you get an overview of all functions provided by metabodecon.
Documentation
metabodecon’s documentation is available at spang-lab.github.io/metabodecon. It includes pages about