Compare multiple metagenomes

[SDPA_Pet]

Hi I think I asked this question here before, but I never got a good answer. I have a annotated metagenome dataset. Basically, it is an abundance speed sheet.

Like this:
sample 1 sample 2 sample 3 sample 4
COG001 1 2 4 3

COG002 1 1 1 1

.
.
.

Each column represents a metagenome. Each row means the number of that COG gene find in each metagenome.

Sample is my query genome. I would like to do analysis so that I can find all of enriched COG genes in my sample 1 (i.e. over-represented genes). It can be multiple comparison with FDR correction P value too (S1 VS S2, S1 VS S3...)

I was wondering if any one has done this before in R or other software. If you did it in R can you tell me which R package you use. Can you share the R code with me?

I find a R package called "ShotgunFunctionalizeR", but it can only do two sample comparison.

Thanks,
Ben

[SDPA_Pet]

Any has done this before?

Thanks

[SDPA_Pet]

Anyone has done more than three genome comparison?