genecounting               package:gap               R Documentation

_G_e_n_e _c_o_u_n_t_i_n_g _f_o_r _h_a_p_l_o_t_y_p_e _a_n_a_l_y_s_i_s

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

     Gene counting for haplotype analysis with missing data

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

     genecounting(data,weight=NULL,convll=1,handle.miss=0,eps=0.00001,maxit=50,pl=0.001)

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

    data: genotype table

  weight: a column of frequencies

  convll: set convergence criteria according to log-likelihood, if its
          value set to 1

handle.miss: to handle missing data, if its value set to 1

     eps: the actual convergence criteria, with default value 1e-5

   maxit: maximum number of iterations, with default value 50

      pl: criteria for trimming haplotypes according to posterior
          probabilities

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

     The returned value is a list containing:

       h: haplotype frequency estimates under linkage disequilibrium
          (LD)

      h0: haplotype frequency estimates under linkage equilibrium (no
          LD)

    prob: genotype probability estimates

      l0: log-likelihood under linkage equilibrium

      l1: log-likelihood under linkage disequilibrium

   hapid: unique haplotype identifier (defunct, see gc.em)

   npusr: number of parameters according user-given alleles

   npdat: number of parameters according to observed

htrtable: design matrix for haplotype trend regression (defunct, see
          gc.em)

    iter: number of iterations used in gene counting

converge: a flag indicating convergence status of gene counting

     di0: haplotype diversity under no LD, defined as 1-sum (h0^2)

     di1: haplotype diversity under LD, defined as 1-sum (h^2)

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

     Zhao, J. H., Lissarrague, S., Essioux, L. and P. C. Sham (2002).
     Gene-counting for haplotype analysis with missing genotypes.
     Bioinformatics 18(12):1694-1695

     Zhao, J. H. and P. C. Sham (2003). Generic number systems and
     haplotype analysis. Comp Meth Prog Biomed 70: 1-9

_N_o_t_e:

     adapted from GENECOUNTING

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

     Jing hua Zhao

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

     'gc.em', 'kbyl'

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

     ## Not run: 
     # Now we use the HLA data for testing
     data(hla)
     hla.gc<-genecounting(hla[,3:8])
     summary(hla.gc)
     hla.gc$l0
     hla.gc$l1

     # Now we use ALDH2 data
     data(aldh2)
     aldh2.gc<-genecounting(aldh2[,3:6],handle.miss=1)
     summary(aldh2.gc)
     aldh2.gc$l0
     aldh2.gc$l1
     ## End(Not run)

