inbreeding            package:GeneticsPed            R Documentation

_I_n_b_r_e_e_d_i_n_g _c_o_e_f_f_i_c_i_e_n_t

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

     'inbreeding' calculates inbreeding coefficients of individuals in
     the pedigree

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

     inbreeding(x, method="meuwissen", sort=TRUE, names=TRUE, ...)

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

       x: pedigree object

  method: character, method of calculation "tabular", "meuwissen" or
          "sargolzaei", see details

    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 vector have names; this can be used
          to get leaner returned object

     ...: arguments for other methods

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

     Coefficient of inbreeding (F) represents probability that two
     alleles on a loci are identical by descent (Wright, 1922; Falconer
     and Mackay, 1996). Wright (1922) showed how F can be calculated
     but his method of paths is not easy to wrap in a program.
     Calculation of F can also be performed using tabular method for
     setting the additive relationship matrix (Henderson, 1976), where
     F_i = A_{ii} - 1. Meuwissen and Luo (1992) and VanRaden (1992)
     developed faster algorithms for F calculation. Wiggans et al.
     (1995) additionally explains method in VanRaden (1992). Sargolzaei
     et al. (2005) presented yet another fast method.

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

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

     A vector of length n with inbreeding coefficients, where n is
     number of subjects in 'x'

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

     Gregor Gorjanc and Dave A. Henderson

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

     Falconer, D. S. and Mackay, T. F. C. (1996) Introduction to
     Quantitative Genetics. 4th edition. Longman, Essex, U.K. <URL:
     http://www.amazon.com/gp/product/0582243025>

     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

     Meuwissen, T. H. E. and Luo, Z. (1992) Computing inbreeding
     coefficients in large populations. _Genetics Selection and
     Evolution_ *24*:305-313

     Sargolzaei, M. and Iwaisaki, H. and Colleau, J.-J. (2005) A fast
     algorithm for computing inbreeding coefficients in large
     populations. _Journal of Animal Breeding and Genetics_
     *122*(5):325-331 <URL:
     http://dx.doi.org/10.1111/j.1439-0388.2005.00538.x>

     VanRaden, P. M. (1992) Accounting for inbreeding and crossbreeding
     in genetic evaluation for large populations. _Journal of Dairy
     Science_ 75(11):3136-3144 <URL:
     http://jds.fass.org/cgi/content/abstract/75/11/3136>

     Wiggans, G. R. and VanRaden, P. M. and Zuurbier, J. (1995)
     Calculation and use of inbreeding coefficients for genetic
     evaluation of United States dairy cattle. _Journal of Dairy
     Science_ *78*(7):1584-1590 <URL:
     http://jds.fass.org/cgi/content/abstract/75/11/3136>

     Wright, S. (1922) Coefficients of inbreeding and relationship.
     _American Naturalist_ 56:330-338

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

     'Pedigree', 'relationshipAdditive', 'kinship' and 'geneFlowT'

_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(inbreeding(x=x2.1))

       ## Compare the speed
       ped <- generatePedigree(nId=25)
       system.time(inbreeding(x=ped))
       # system.time(inbreeding(x=ped, method="sargolzaei")) # not yet implemented
       system.time(inbreeding(x=ped, method="tabular"))

