Pathway enrichment analysis bacterial genome
Hi,
I have created a counts matrix from an experiment with 20 bacterial samples (10 bacteria treated and 10 not treated).
I would like to identify the pathways that over and under represented upon treatment.
So far i have created a counts matrix as follows. Each row represents an EC number found in each bacterial sample.
SAMPLE_1 SAMPLE_2 SAMPLE_3.....
EC.1.1.1.2 300 100 50
EC.2.3.2.1 100 100 100
.....
How can i transform this dataframe into metabolic pathways and get the enrich pathways ?
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