read_and_process_KO_table

This function reads a KO sample table (wide format), validates its contents against
pathway information, and returns a filtered table containing only KOs present in both datasets.

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

read_and_process_KO_table function

<dl><dt>in_KO_Sample_wide</dt>
<dd>Character string specifying the path to the input KO sample table file.
Should be a tab-delimited file with KO identifiers as row names.</dd>
<dt>pathway_infor</dt>
<dd>Data frame containing pathway information, see examples.</dd></dl>

Arguments

Read and Process KO Sample Table with Pathway Information — read_and_process_KO_table

<dl>

<dt>in_KO_Sample_wide</dt>
<dd>Character string specifying the path to the input KO sample table file.
Should be a tab-delimited file with KO identifiers as row names.</dd>


<dt>pathway_infor</dt>
<dd>Data frame containing pathway information, see examples.</dd>

</dl>

read_and_process_KO_table: Read and Process KO Sample Table with Pathway Information

Description

Usage

Value

Arguments