read_and_process_pathway_infor

This function reads a tab-delimited file containing KEGG pathway information,
performs data validation and cleaning, and returns a processed data frame.

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_pathway_infor function

<dl><dt>in_KO_pathway_ref</dt>
<dd>Character string specifying the path to the input file.
The file should be a tab-delimited text file containing KEGG pathway information,
with a header row and at least one column named "Module_Entry".</dd></dl>

Arguments

Read and process Pathway information dataframe — read_and_process_pathway_infor

<dl>

<dt>in_KO_pathway_ref</dt>
<dd>Character string specifying the path to the input file.
The file should be a tab-delimited text file containing KEGG pathway information,
with a header row and at least one column named "Module_Entry".</dd>

</dl>

read_and_process_pathway_infor: Read and process Pathway information dataframe

Description

Usage

Value

Arguments