TDT: Gene and gamete flow matrices

In GeneticsPed: Pedigree and genetic relationship functions

Description

geneFlowT and geneFlowTinv creates gene flow matrix (T) and its inverse (Tinv), while gameteFlowM creates gamete flow matrix (M). mendelianSamplingD creates a mendelian sampling covariance matrix (D).

Usage

geneFlowT(x, sort=TRUE, names=TRUE, ...)
geneFlowTinv(x, sort=TRUE, names=TRUE, ...)
gameteFlowM(x, sort=TRUE, names=TRUE, ...)
mendelianSamplingD(x, matrix=TRUE, names=TRUE, ...)

Arguments

x	Pedigree
sort	logical, for the computation the pedigree needs to be sorted, but results are sorted back to original sorting (sort=TRUE) or not (sort=FALSE)
names	logical, should returned matrix have row/colnames; this can be used to get leaner matrix
matrix	logical, should returned value be a diagonal matrix or a vector
...	arguments for other methods

Details

geneFlowT returns a matrix with coefficients that show the flow of genes from one generation to the next one etc. geneFlowTinv is simply the inverse of geneFlowT, but calculated as I - M, where M is gamete flow matrix with coefficients that represent parent gamete contribution to their offspring. mendelianSamplingD is another matrix (D) for construction of relationship additive matrix via decomposition i.e. A=TDT' (Henderson, 1976). Mrode (2005) has a very nice introduction to these concepts.

Take care with sort=FALSE, names=FALSE. It is your own responsibility to assure proper handling in this case.

Value

Matrices of n * n dimension, with coeficients as described in the details, where n is number of subjects in x

Author(s)

Gregor Gorjanc

References

Henderson, C. R. (1976) A simple method for computing the inverse of a numerator relationship matrix used in prediction of breeding values. Biometrics 32(1):69-83

Mrode, R. A. (2005) Linear models for the prediction of animal breeding values. 2nd edition. CAB International. ISBN 0-85199-000-2 http://www.amazon.com/gp/product/0851990002

See Also

Pedigree, relationshipAdditive, kinship and inbreeding

Examples

if(require(gdata))
  data(Mrode2.1)
  Mrode2.1$dtB <- as.Date(Mrode2.1$dtB)
  x2.1 <- Pedigree(x=Mrode2.1, subject="sub", ascendant=c("fat", "mot"),
                   ascendantSex=c("M", "F"), family="fam", sex="sex",
                   generation="gen", dtBirth="dtB")

  fractions(geneFlowT(x2.1))
  fractions(geneFlowTinv(x2.1))
  fractions(gameteFlowM(x2.1))
  mendelianSamplingD(x2.1)

GeneticsPed documentation built on Nov. 8, 2020, 5:54 p.m.