scale_vast

Scales the intensities of all features using
$$\widetilde{x}_{ij}=\frac{x_{ij}-\overline{x}_{i}}{s_i}\cdot \frac{\overline{x}_{i}}{s_i}$$
where $\widetilde{x}_{ij}$ is the intensity of sample $j$, feature $i$ after scaling,
$x_{ij}$ is the intensity of sample $j$, feature $i$ before scaling, $\overline{x}_{i}$ is the mean of intensities of feature $i$ across all samples
and ${s_i}$ is the standard deviation of intensities of feature $i$ across all samples. Note that $\frac{\overline{x}_{i}}{s_i} = \frac{{1}}{CV}$ where CV is the coefficient of variation across all samples.
<code>scale_vast_grouped</code> is a variation of this function that uses a group-specific coefficient of variation.
In other words, it performs autoscaling (<code>scale_auto</code>) and divides by the coefficient of variation, thereby reducing the importance of features with a poor reproducibility.

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

scale_vast function

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

Arguments

Scale intensities of features using vast scaling — scale_vast

<dl>

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

</dl>

scale_vast: Scale intensities of features using vast scaling

Description

Usage

Value

Arguments

References

Examples