abalvarenga/LDanalysis

Pipeline used to calculate linkage disequilibrium (LD) and data vizualization of LD. That was one of steps used for results of the LD's research in Santa Inês ovine population : https://www.nature.com/articles/s41598-018-27259-7

LDanalysis

Pipeline in R used to calculate linkage disequilibrium (LD) and data vizualization of LD. That was one of steps used for results of the LD's research in Santa Inês ovine population : https://www.nature.com/articles/s41598-018-27259-7

*** Description of files ***

geno:

        1. SNP ID
        2. Chromosome
        3. SNP position
        4. Genotype of animal 1, nitrogene basis. Example: GG, CC, AC, etc.
        5. Genotype of animal 2, nitrogene basis. Example: GG, CC, AC, etc.  
        ...
        column i.  Genotype of animal i, nitrogene basis. Example: GG, CC, AC, etc.

Assuming i is the number of animals. Missing values assumed as "--".

feno_teste2.txt:

        1. Animal ID
        2. Sex, as 1 and 0
        3. Trait

SNP_Map.txt:

        1. SNP ID
        2. Chromosome
        3. SNP position