any way to merge functions of kegg orthologs database?
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8 weeks ago

Hello I'm parsing a metagenomic dataset of oral microbiome data. I used picrust2 to predict functions from 16S gene amplicon data and I need to plot the microbial predicted functions.

The problem is that I have a a table of samples and related functions that looks like the following table:

sample_picrust_output

the functions column is to the KEGG orthologs database function IDs, the second column is the description of the function and the other columns are to the abundances of the functions found per each sample.

The problem is that I founded that there are 7950 functions along the metagenomic datasets so for plotting purposes I cannot show all the almost 8000 functions.

A solution that I thing is the most appropriate one is to merge all the rows (functions) that have a similar function or can be merged into a function category (lets say join all the functions to simpler categories such as "protein metabolism" "membrane transport" "central metabolism" and so on)

Is there a way to merge functions abundances to a broader category as the ones I exampled to make better plots?

Thsnks for your time!

functional-profile metagenomics data-wrangling • 139 views
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