Question: Different methodology in microbiome-GWAS
0
gravatar for F
16 months ago by
F3.4k
Iran
F3.4k wrote:

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

gwas R mirkat gemma • 510 views
ADD COMMENTlink modified 16 months ago • written 16 months ago by F3.4k

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

ADD REPLYlink modified 16 months ago • written 16 months ago by F3.4k
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