add_rows_if_not_exists

This function checks if specified rows exist in a data frame, and if not,
adds them with all values set to 0. Useful for ensuring consistent KO
representation across samples.

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

add_rows_if_not_exists function

<dl><dt>module_abundance</dt>
<dd>A data frame with row names representing KO identifiers
(e.g., K numbers) and numeric abundance values</dd>
<dt>add_rows</dt>
<dd>A character vector of row names (KO identifiers) that should be
present in the output. Defaults to c("K14126","K14128","K14127")</dd></dl>

Arguments

Add Missing Rows to a Data Frame — add_rows_if_not_exists

<dl>

<dt>module_abundance</dt>
<dd>A data frame with row names representing KO identifiers
(e.g., K numbers) and numeric abundance values</dd>


<dt>add_rows</dt>
<dd>A character vector of row names (KO identifiers) that should be
present in the output. Defaults to c("K14126","K14128","K14127")</dd>

</dl>

add_rows_if_not_exists: Add Missing Rows to a Data Frame

Description

Usage

Value

Arguments