htr                   package:gap                   R Documentation

_H_a_p_l_o_t_y_p_e _t_r_e_n_d _r_e_g_r_e_s_s_i_o_n

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

     Haplotype trend regression (with permutation)

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

     htr(y,x,n.sim=0)

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

       y: a vector of phenotype

       x: a haplotype table

   n.sim: the number of permutations

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

     The returned value is a list containing:

       f: the F statistic for overall association

       p: the p value for overall association

      fv: the F statistics for individual haplotypes

      pi: the p values for individual haplotypes

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

     Zaykin DV, Westfall PH, Young SS, Karnoub MA, Wagner MJ, Ehm MG
     (2002) Testing association of statistically inferred haplotypes
     with  discrete and continuous traits in samples of unrelated
     individuals. Hum. Hered. 53:79-91

_N_o_t_e:

     adapted from emgi.cpp, a pseudorandom number seed will be added on

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

     Dimitri Zaykin, Jing hua Zhao

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

     'htr'

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

     ## Not run: 
     # 26-10-03
     test2<-read.table("test2.dat")
     y<-test2[,1]
     x<-test2[,-1]
     y<-as.matrix(y)
     x<-as.matrix(x)
     htr.test2<-htr(y,x)
     htr.test2
     htr.test2<-htr(y,x,n.sim=10)
     htr.test2

     # 13-11-2003
     data(apoeapoc)
     apoeapoc.gc<-gc.em(apoeapoc[,5:8])
     y<-apoeapoc$y
     for(i in 1:length(y)) if(y[i]==2) y[i]<-1
     htr(y,apoeapoc.gc$htrtable)
     ## End(Not run)

