Package: MGMS2 1.0.2

George Wendt

MGMS2: 'MGMS2' for Polymicrobial Samples

A glycolipid mass spectrometry technology has the potential to accurately identify individual bacterial species from polymicrobial samples. To develop bacterial identification algorithms (e.g. machine learning) using this glycolipid technology, it is necessary to generate a large number of various in-silico polymicrobial mass spectra that are similar to real mass spectra. 'MGMS2' (Membrane Glycolipid Mass Spectrum Simulator) generates such in-silico mass spectra, considering errors in m/z (mass-to-charge ratio) and variances of intensity values, occasions of missing signature ions, and noise peaks. It estimates summary statistics of monomicrobial mass spectra for each strain or species and simulates polymicrobial glycolipid mass spectra using the summary statistics of monomicrobial mass spectra. References: Ryu, S.Y., Wendt, G.A., Chandler, C.E., Ernst, R.K. and Goodlett, D.R. (2019) <doi:10.1021/acs.analchem.9b03340> "Model-based Spectral Library Approach for Bacterial Identification via Membrane Glycolipids." Gibb, S. and Strimmer, K. (2012) <doi:10.1093/bioinformatics/bts447> "MALDIquant: a versatile R package for the analysis of mass spectrometry data."

Authors:So Young Ryu [aut], George Wendt [cre]

MGMS2_1.0.2.tar.gz
MGMS2_1.0.2.tar.gz(r-4.5-noble)MGMS2_1.0.2.tar.gz(r-4.4-noble)
MGMS2_1.0.2.tgz(r-4.4-emscripten)MGMS2_1.0.2.tgz(r-4.3-emscripten)
MGMS2.pdf |MGMS2.html
MGMS2/json (API)

# Install 'MGMS2' in R:
install.packages('MGMS2', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.70 score 2 scripts 126 downloads 8 exports 7 dependencies

Last updated 5 years agofrom:a9249e79c5. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 27 2024
R-4.5-linuxOKOct 27 2024

Exports:characterize_peakcreate_insilico_mixture_templategather_summarygather_summary_fileprocess_monospectrasimulate_many_poly_spectrasimulate_poly_spectrasummarize_monospectra

Dependencies:base64encdigestMALDIquantMALDIquantForeignreadBrukerFlexDatareadMzXmlDataXML

Readme and manuals

Help Manual

Help pageTopics
characterize_peakcharacterize_peak
create_insilico_mixture_templatecreate_insilico_mixture_template
filtermassfiltermass
gather_summarygather_summary
gather_summary_filegather_summary_file
preprocessMSpreprocessMS
process_monospectraprocess_monospectra
simulate_ind_spec_singlesimulate_ind_spec_single
simulate_many_poly_spectrasimulate_many_poly_spectra
simulate_poly_spectrasimulate_poly_spectra
summarize_monospectrasummarize_monospectra
summary_monosummary_mono