Different methodology in microbiome-GWAS

Question

[zizigolu]

Hi,

I just wonder if somebody in this forum has already used MiRKAT R package for microbiome-GWAS.

There are GEMMA, microbiome GWAS in this context but by Linux. As MiRKAT documentation is very hard to understand, my question is if this is my microbiom

              Acaryochloris Achromobacter Acidiphilium Acidisphaera

Sample1             23             1            0            4                 
Sample2              0             0            2            0                 
Sample3              4             0            4            0                 
Sample4              0            30            0            5                 
Sample5             11             0            5            0                 
Sample6              0             0            0            0

and this is my bim file

##            chromosome   snp.name cM  position allele.1 allele.2
## rs4579145           4  rs4579145  0  78303781        T        C
## rs2768995           6  rs2768995  0   6911315        C        T
## rs10125738          9 rs10125738  0 101066136        A        G
## rs888263           18   rs888263  0  12750253        G        A
## rs7639361           3  rs7639361  0  80138205        A        C
## rs2430512          17  rs2430512  0  69675940        T        C

MiRKAT has meta data option (I attached screenshot), then where I should put my SNP data to calculate correlation???

https://www.imageupload.co.uk/image/EARK

Thank you

[zizigolu]

MiRKAT developer said that "If you code your SNP data by 0/1/2, then it should be your y if you are interested in the association between micro biome and the SNP. The metadata that you want to adjust for is in the X covariates. "

but got too complicated