HWE.chisq            package:GeneticsBase            R Documentation

_H_a_r_d_y-_W_e_i_n_b_e_r_g _E_q_u_i_l_i_b_r_i_u_m _S_i_g_n_i_f_i_c_a_n_c_e _t_e_s_t _f_o_r _a _b_i_a_l_l_e_l_i_c _l_o_c_u_s

_D_e_s_c_r_i_p_t_i_o_n:

     Hardy-Weinberg Equilibrium Significance test for a biallelic locus
     .

_U_s_a_g_e:

     HWE.chisq(object,
               marker,
               simulate.p.value = TRUE,
               B = 10000, 
               founderOnly=TRUE, 
               ...)

_A_r_g_u_m_e_n_t_s:

  object: a geneSet object.

  marker: marker name for the biallelic locus.

simulate.p.value: a logical indicating whether to compute p-values by
          Monte Carlo simulation.

       B: an integer specifying the number of replicates used in the
          Monte Carlo test. Defaults to 10000.

founderOnly: Indicates if only founders are used to do the test.

     ...: Othere arguments used by the function 'chisq.test'.

_V_a_l_u_e:

     The values of the function 'HWE.chisq' is the same as those of the
     function 'chisq.test'. Part of the values are listed below:  

statistic: the value the chi-squared test statistic.

parameter: the degrees of freedom of the approximate chi-squared
          distribution of the test statistic, 'NA' if the p-value is
          computed by Monte Carlo simulation.

 p.value: the p-value for the test.

_A_u_t_h_o_r(_s):

     Gregory R. Warnes gregory.r.warnes@pfizer.com and Nitin Jain
     nitin.jain@pfizer.com

_S_e_e _A_l_s_o:

     'HWE.exact'

_E_x_a_m_p_l_e_s:

     library(GeneticsBase)
     data(CAMP)

     HWE.chisq(CAMP, marker="m654")

