kbyl                   package:gap                   R Documentation

_L_D _s_t_a_t_i_s_t_i_c_s _f_o_r _t_w_o _m_u_l_t_i_a_l_l_e_l_i_c _l_o_c_i

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

     LD statistics for two multiallelic loci

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

     kbyl(n1=2,n2=2,h,n,optrho=2,verbose=FALSE)

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

      n1: number of alleles at marker 1

      n2: number of alleles at marker 2

       h: a vector of haplotype frequencies

       n: number of haplotypes

  optrho: type of contingency table association, 0=Pearson,
          1=Tschuprow, 2=Cramer (default)

 verbose: detailed output of individual statistics

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

     The returned value is a list containing:

      n1: the number of alleles at marker 1

      n2: the number of alleles at marker 2

       h: the haplotype frequency vector

       n: the number of haplotypes

      Dp: D'

   VarDp: variance of D'

Dijtable: table of Dij

VarDijtable: table of variances for Dij

Dmaxtable: table of Dmax

Dijptable: table of Dij'

VarDijptable: table of variances for Dij'

 X2table: table of Chi-squares (based on Dij)

  ptable: table of p values

      x2: the Chi-squared statistic

    seX2: the variance of x2

     rho: the measure of association

     seR: the standard error of rho

  optrho: the method for calculating rho

  klinfo: the Kullback-Leibler information

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

     Bishop YMM, Fienberg SE, Holland PW (1975) Discrete Multivariate
     Analysis - Theory and Practice, The MIT press

     Cramer H (1946) Mathematical Methods of Statistics. Princeton
     Univ. Press

     Zapata C, Carollo C, Rodriquez S (2001) Sampleing variance and
     distribution of the D' measure of overall gametic disequilibrium
     between multiallelic loci. Ann. Hum. Genet. 65: 395-406

     Zhao, JH (2004). 2LD, GENECOUNTING and HAP: Computer programs for
     linkage disequilibrium analysis. Bioinformatics 20:1325-1326

_N_o_t_e:

     adapted from 2ld.c

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

     Jing Hua Zhao

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

     'tbyt'

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

     ## Not run: 

     # two examples in the C program 2LD:
     # two SNPs as in 2by2.dat
     # this can be compared with output from tbyt

     h <- c(0.442356,0.291532,0.245794,0.020319)
     n <- 481*2
     t <- kbyl(2,2,h,n)
     t

     # two multiallelic markers as in kbyl.dat
     # the two-locus haplotype vector is in the file "h"

     h <- scan("h")
     t <- kbyl(9,5,h,213*2,verbose=T)
     ## End(Not run)

