calc_neutral_loss

<a href="https://lifecycle.r-lib.org/articles/stages.html#deprecated"><img src="figures/lifecycle-deprecated.svg?package=metamorphr&version=0.3.0" alt="[Deprecated]"></a>
<code>calc_neutral_loss()</code> is fully replaced by <code>msn_calc_nl</code>.
Calculate neutral loss spectra for all ions with available MSn spectra in <code>data</code>. To calculate neutral losses, MSn spectra are required.
See <code>read_mgf</code>. This step is required for subsequent filtering based on
neutral losses (<code>filter_neutral_loss</code>). Resulting neutral loss spectra are stored in tibbles in a new list column named <code>Neutral_Loss</code>.

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

calc_neutral_loss function

<dl><dt>data</dt>
<dd>A tidy tibble created by <code>read_featuretable</code>.</dd>
<dt>m_z_col</dt>
<dd>Which column holds the precursor m/z? Uses <code>args_data_masking</code>.</dd></dl>

Arguments

<a href='https://lifecycle.r-lib.org/articles/stages.html#deprecated'><img src='figures/lifecycle-deprecated.svg' alt='[Deprecated]' /></a>
<code>calc_neutral_loss()</code> is fully replaced by <code>msn_calc_nl</code>.
Calculate neutral loss spectra for all ions with available MSn spectra in <code>data</code>. To calculate neutral losses, MSn spectra are required.
See <code>read_mgf</code>. This step is required for subsequent filtering based on
neutral losses (<code>filter_neutral_loss</code>). Resulting neutral loss spectra are stored in tibbles in a new list column named <code>Neutral_Loss</code>.

Calculate neutral losses from precursor ion mass and fragment ion masses — calc_neutral_loss

<dl>

<dt>data</dt>
<dd>A tidy tibble created by <code>read_featuretable</code>.</dd>


<dt>m_z_col</dt>
<dd>Which column holds the precursor m/z? Uses <code>args_data_masking</code>.</dd>

</dl>

calc_neutral_loss: Calculate neutral losses from precursor ion mass and fragment ion masses

Description

Usage

Value

Arguments

Examples