geneFlowT            package:GeneticsPed            R Documentation

_G_e_n_e _a_n_d _g_a_m_e_t_e _f_l_o_w _m_a_t_r_i_c_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     '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).

_U_s_a_g_e:

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

_A_r_g_u_m_e_n_t_s:

       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

_D_e_t_a_i_l_s:

     '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.

_V_a_l_u_e:

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

_A_u_t_h_o_r(_s):

     Gregor Gorjanc

_R_e_f_e_r_e_n_c_e_s:

     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 <URL: http://www.amazon.com/gp/product/0851990002>

_S_e_e _A_l_s_o:

     'Pedigree', 'relationshipAdditive', 'kinship' and 'inbreeding'

_E_x_a_m_p_l_e_s:

       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)

