read_mgf

<a href="https://www.matrixscience.com/help/data_file_help.html">MGF files</a> allow the storage of MS/MS spectra. This
function reads them into a tidy tibble. Each variable is stored in a column and each ion (observation) is stored in a separate row.
MS/MS spectra are stored in a list column named MSn. 
Please note that <a href="https://fiehnlab.ucdavis.edu/projects/lipidblast/mgf-files">MGF files are software-specific</a> so the variables
and their names may vary. This function was developed with the GNPS file format exported from <a href="https://mzio.io/mzmine-news/">mzmine</a> in mind. 
If you encounter any bugs please report them: <a href="https://github.com/yasche/metamorphr/issues">https://github.com/yasche/metamorphr/issues</a>

Facilitate tasks typically encountered during metabolomics data analysis including data import, filtering, missing value imputation (Stacklies et al. (2007) <doi:10.1093/bioinformatics/btm069>, Stekhoven et al. (2012) <doi:10.1093/bioinformatics/btr597>, Tibshirani et al. (2017) <doi:10.18129/B9.BIOC.IMPUTE>, Troyanskaya et al. (2001) <doi:10.1093/bioinformatics/17.6.520>), normalization (Bolstad et al. (2003) <doi:10.1093/bioinformatics/19.2.185>, Dieterle et al. (2006) <doi:10.1021/ac051632c>, Zhao et al. (2020) <doi:10.1038/s41598-020-72664-6>) transformation, centering and scaling (Van Den Berg et al. (2006) <doi:10.1186/1471-2164-7-142>) as well as statistical tests and plotting. 'metamorphr' introduces a tidy (Wickham et al. (2019) <doi:10.21105/joss.01686>) format for metabolomics data and is designed to make it easier to build elaborate analysis workflows and to integrate them with 'tidyverse' packages including 'dplyr' and 'ggplot2'.

Yannik Schermer

metamorphr

Tidy and Streamlined Metabolomics Data Workflows

read_mgf function

<dl><dt>file</dt>
<dd>The path to the MGF file.</dd>
<dt>show_progress</dt>
<dd>A <code>logical</code> indicating whether the progress of the import should be printed to the console. Only important for large MGF files.</dd></dl>

Arguments

<a href='https://www.matrixscience.com/help/data_file_help.html'>MGF files</a> allow the storage of MS/MS spectra. This
function reads them into a tidy tibble. Each variable is stored in a column and each ion (observation) is stored in a separate row.
MS/MS spectra are stored in a list column named MSn. 
Please note that <a href='https://fiehnlab.ucdavis.edu/projects/lipidblast/mgf-files'>MGF files are software-specific</a> so the variables
and their names may vary. This function was developed with the GNPS file format exported from <a href='https://mzio.io/mzmine-news/'>mzmine</a> in mind. 
If you encounter any bugs please report them: <a href='https://github.com/yasche/metamorphr/issues'>https://github.com/yasche/metamorphr/issues</a>

Read a MGF file into a tidy tibble — read_mgf

<dl>

<dt>file</dt>
<dd>The path to the MGF file.</dd>


<dt>show_progress</dt>
<dd>A <code>logical</code> indicating whether the progress of the import should be printed to the console. Only important for large MGF files.</dd>

</dl>

read_mgf: Read a MGF file into a tidy tibble

Description

Usage

Value

Arguments

Examples