convert_abundance_to_presence

Transforms a numeric abundance matrix into a binary presence/absence matrix,
where 1 indicates presence (abundance &gt; 0) and 0 indicates absence.
Preserves row names as Orthology_Entry column in the output.

Provides tools for analyzing metabolic pathway completeness, abundance, and transcripts
using KEGG Orthology (KO) data from (meta)genomic and (meta)transcriptomic studies.
Supports both completeness (presence/absence) and abundance-weighted analyses.
Includes built-in KEGG reference datasets. For more details see Li et al. (2023) <doi:10.1038/s41467-023-42193-7>.

Liuyang Li

mclink

Metabolic Pathway Completeness and Abundance Calculation

convert_abundance_to_presence function

<dl><dt>module_abundance</dt>
<dd>A data frame containing KO abundance data, must include:
- Rows named by Orthology_Entry (KO identifiers)
- Numeric columns representing sample abundances
- An Orthology_Entry column</dd></dl>

Arguments

Convert Abundance Values to Presence/Absence Indicators — convert_abundance_to_presence

<dl>

<dt>module_abundance</dt>
<dd>A data frame containing KO abundance data, must include:
- Rows named by Orthology_Entry (KO identifiers)
- Numeric columns representing sample abundances
- An Orthology_Entry column</dd>

</dl>

convert_abundance_to_presence: Convert Abundance Values to Presence/Absence Indicators

Description

Usage

Value

Arguments