Host-bacteria Correlation analysis

Question

[zizigolu]

Hi,

I have OTU table.txt where every cell contains a percentage and the table is divided into three cell type IL, TR and RE and the for each cell type it would be divided into the 6 Taxonomic levels (Class Family Genus Order Phylum Species). Furthermore for every level I have the three different amplicion (v1v2 v3v4 v5v6). I also have BED/bim/fam files. How I can perform correlation analysis and extract SNPs related to bacteria????? I have already installed PLINK.

Thank you

[zizigolu]

I found a nice tutorial all R based for GWAS, I hope I could adapt this for my question too

http://www.stat-gen.org/tut/tut_intro.html