Pathway enrichment analysis bacterial genome

Question

[David]

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 ?