camult / GDmat

Calculates Additive and Dominance Relationship Matrices

GRM: Calculates the realized additive relationship matrix

Description

Calculates realized additive (genomic) relationship matrix.

Usage

GRM(X, smallValue)

Arguments

Argument	Description
X	is a (numeric, $n$ ) matrix of genotypes with a number of rows identical to the number of SNPs (m) and a number of columns identical to the number of genotyped individuals (n). Values in the matrix are 0 and 2 for homozygous and 1 for heterozygous.
smallValue	is a numeric valeu that can be added to the diagonal of the genomic relationship matrix (GRM).

References

VanRaden, Paul M. Efficient methods to compute genomic predictions. Journal of dairy science 91.11 (2008): 4414-4423.

Su G, Christensen OF, Ostersen T, Henryon M, Lund MS. 2012. Estimating Additive and Non-Additive Genetic Variances and Predicting Genetic Merits Using Genome-Wide Dense Single Nucleotide Polymorphism Markers. PLoS ONE 7(9): e45293. doi:10.1371/journal.pone.0045293

Examples

 ## Not to run ##
 
 ## GRM(X, smallValue)
 
 ## End(Not run)
 

DRM: Calculates the realized dominance relationship matrix

Description

Calculates realized dominance relationship matrix.

Usage

DRM(X)

Arguments

Argument	Description
X	is a (numeric, $n$ ) matrix of genotypes with a number of rows identical to the number of SNPs (m) and a number of columns identical to the number of genotyped individuals (n). Values in the matrix are 0 and 2 for homozygous and 1 for heterozygous.

References

VanRaden, Paul M. Efficient methods to compute genomic predictions. Journal of dairy science 91.11 (2008): 4414-4423.

Su G, Christensen OF, Ostersen T, Henryon M, Lund MS. 2012. Estimating Additive and Non-Additive Genetic Variances and Predicting Genetic Merits Using Genome-Wide Dense Single Nucleotide Polymorphism Markers. PLoS ONE 7(9): e45293. doi:10.1371/journal.pone.0045293

Examples

 ## Not to run ##
 
 ## DRM(X)
 
 ## End(Not run)
 

NRM: Calculates the Pedigree-based Additive Relationship Matrix

Description

Calculates the the Pedigree-based Additive Relationship Matrix. This is twice the pedigree based kinship matrix.

Usage

NRM(Pedig)

Arguments

Argument	Description
Pedig	Data frame containing the Pedigree. The data frame has columns (1) Individual, (2) Sire, (3) Dam. Missing parents are coded as NA.

Value

Additive relationship matrix.

Examples

 ## Not to run ##
 
 ## NRM(Pedig)
 
 ## End(Not run)