calculate_log2_fold_change

Calculates log2 fold change between two groups with proper handling
of zero values using a data-driven pseudocount approach.

internal

Provides a convenient way to analyze and visualize 'PICRUSt2' output with pre-defined plots and functions. Allows for generating statistical plots about microbiome functional predictions and offers customization options. Features a one-click option for creating publication-level plots, saving time and effort in producing professional-grade figures. Streamlines the 'PICRUSt2' analysis and visualization process. For more details, see Yang et al. (2023) <doi:10.1093/bioinformatics/btad470>.

Chen Yang

ggpicrust2

Make 'PICRUSt2' Output Analysis and Visualization Easier

calculate_log2_fold_change function

<dl><dt>mean1</dt>
<dd>Numeric. Mean abundance of group 1 (reference/control)</dd>
<dt>mean2</dt>
<dd>Numeric. Mean abundance of group 2 (comparison/treatment)</dd>
<dt>pseudocount</dt>
<dd>Optional numeric. If NULL, calculated from reference_values</dd>
<dt>reference_values</dt>
<dd>Optional numeric vector for calculating pseudocount</dd></dl>

Arguments

Calculate log2 fold change with consistent pseudocount handling — calculate_log2_fold_change

<dl>

<dt>mean1</dt>
<dd>Numeric. Mean abundance of group 1 (reference/control)</dd>


<dt>mean2</dt>
<dd>Numeric. Mean abundance of group 2 (comparison/treatment)</dd>


<dt>pseudocount</dt>
<dd>Optional numeric. If NULL, calculated from reference_values</dd>


<dt>reference_values</dt>
<dd>Optional numeric vector for calculating pseudocount</dd>

</dl>

calculate_log2_fold_change: Calculate log2 fold change with consistent pseudocount handling

Description

Usage

Value

Arguments

Details