TDT: Gene and gamete flow matrices

Description Usage Arguments Details Value Author(s) References See Also Examples

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

1
2
3
4

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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
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. 17, 2017, 1:13 p.m.