Regarding genotype input format of mrMLM for GWAS analysis?

Question

[majeedaasim]

I intend to use mrMLM for GWAS analysis. I have read the package in details and everything is clear, except one thing:

The issue is regarding the coding of genotypic file. In the manual, it is mentioned that:

The fourth column, named "genotype for code 1", indicates reference base for code variable x = 1

What is to write in this column? Is it the reference allele? or something else?

Also, regarding the coding of the genotypes, it is mentioned that; For each marker, homozygous genotypes are expressed by 1 and -1, respectively, and the heterozygous and missing genotypes are indicated by zero.

What I understand from this is mentioned below:

The code is

• 1, if genotype is homozygous for the reference allele (if fourth column is the reference allele)
• -1, if the genotype is homozygous for the alternate allele.
• 0 for both heterozygous
• 0 for the NAs

Please clarify, if I am correct, else need your help for correct coding of my genotype file

Answer 1

[Dana]

you can find the answer in the user manual of the article (File S3. User manual for mrMLM v4.0.2):

"genotype for code 1", indicates reference base for code variable x = 1. Among the remaining columns, each column lists all the genotypes for one individual, and the first row shows the individual names. For each marker, homozygous genotypes are expressed by 1 and -1, respectively, and the heterozygous and missing genotypes are indicated by zero. If the base for the first individual is missing, the base firstly observed in this row is what we list.