Documentation

Genetic Relationship Matrix Computation

Description

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DISSECT can compute the genetic relationship matrix (GRM) in a population from a set of SNPs. Genetic relationship between individuals i and j is computed as:\[A_{ij}=\frac{1}{N}\sum_{k=1}^{N}{\frac{ \left(s_{ik} – 2p_k\right) \left(s_{jk} – 2p_k\right) }{ 2p_k\left(1-p_k\right) }}\] where \(s_{ik}\) is the number of copies of the reference allele for the SNP k of the individual j and \(p_k\) is the frequency of the reference allele for the SNP k and N is the number of SNPs.
DISSECT can store the resultant GRM or their eigendecomposition in a file for further analyses.

Please, note that at the current version, DISSECT does not make any assumption about chromosomes, and use the same equation for computing the GRM in all of them.

Examples

Compute the GRM from genotypes in genotypes file

dissect --make-grm --bfile genotypes --out results

Compute the GRM from a list of genotype files. Method 1 is used: All genotype files will be joined before computing GRM.

dissect --make-grm --bfile-list genotypes --grm-join-method 1 --out results

Options

 

Analysis Options

--make-grm Compute the Genetic Relationship Matrix

Input Options

--bfile f Specify a genotypes file.
--bfile-list f Specify a file with a list of genotypes files. This option usually uses much less memory since not all genotypes must be loaded at same time.

Output Options

--out f Specify the base name for output files.

 

Others

--grm-join-method n Specify how GRM will be constructed when genotypes are specified as a list of genotypes files when using the --bfile-list option. n = 0 creates a GRM for each genotype file. Then, add GRMs together (default). n = 1 joins all genotype files before computing GRM. May need much more memory.
--diagonalize After computation, GRM is diagonalized and their eigenvectors and eigenvalues are stored. Diagonal GRMs can only be used in single MLM analyses.
--store-both If GRM is diagonalized, this option forces storing also the original (non-diagonal) GRM. The files are tagged with .nondiagonal

Output description

GRM computation generates files that store the computed GRMs. This files are described in Input Files