impute_rf

Basically a wrapper function around <code>missForest::</code><code>missForest</code>. Imputes missing values using the random forest algorithm.

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

impute_rf function

<dl><dt>data</dt>
<dd>A tidy tibble created by <code>read_featuretable</code>.</dd>
<dt>random_seed</dt>
<dd>A seed for the random number generator. Can be an integer or <code>NULL</code> (in case no particular seed should be used) but for reproducibility reasons it is strongly advised to provide an integer.</dd>
<dt>...</dt>
<dd>Additional parameters passed to <code>missForest</code>.</dd></dl>

Arguments

Impute missing values using random forest — impute_rf

<dl>

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


<dt>random_seed</dt>
<dd>A seed for the random number generator. Can be an integer or <code>NULL</code> (in case no particular seed should be used) but for reproducibility reasons it is strongly advised to provide an integer.</dd>


<dt>...</dt>
<dd>Additional parameters passed to <code>missForest</code>.</dd>

</dl>

impute_rf: Impute missing values using random forest

Description

Usage

Value

Arguments

References

Examples