HWE               package:GeneticsBase               R Documentation

_T_e_s_t _t_h_e _s_i_g_n_i_f_i_c_a_n_c_e_s _o_f _H_a_r_d_y-_W_e_i_n_b_e_r_g _E_q_u_i_l_i_b_r_i_u_m (_d_i_s)_e_q_u_i_l_i_b_r_i_u_m) _s_t_a_t_i_s_t_i_c_s

_D_e_s_c_r_i_p_t_i_o_n:

     Test the significances of Hardy-Weinberg Equilibrium
     (dis)equilibrium) statistics for each marker in a data set.

_U_s_a_g_e:

     HWE(object, 
         test = c("exact", "permutation", "chisq"), 
         B = 10000, 
         R = 1000, 
         correct = TRUE, 
         conf = c(0.95), 
         na.rm = TRUE, 
         founderOnly = TRUE, 
         ...) 

_A_r_g_u_m_e_n_t_s:

  object: a geneSet object.

    test: specifys the test method. Available methods are "exact",
          "permutation", "chisq".

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

       R: Number of bootstrap iterations to use when computing the
          confidence interval. Defaults to 1000.

 correct: see 'diseq.ci'.

    conf: Confidence level to use when computing the confidence level
          for linkage disequilibrium measures.  Defaults to 0.95,
          should be in (0,1).

   na.rm: logical. Should missing values be removed?

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 function 'HWE' returns a list: 

 "diseq": a character string.

    call: the matched call.

     "D": a matrix with $m$ rows and $3+p$ columns, where $m$ is the
          number of markers in the geneSet, $p$ is the number of
          elements of the argument 'conf'. The first column is the
          estimated "D". The next $p$ columns are estimated confidence
          limits for the confidence levels specified in the argument
          'conf'. The last two columns are the sample size and the
          p-value of the test that "D" is equal to zero.

    "D'": a matrix with $m$ rows and $3+p$ columns, where $m$ is the
          number of markers in the geneSet, $p$ is the number of
          elements of the argument 'conf'. The first column is the
          estimated "D'". The next $p$ columns are estimated confidence
          limits for the confidence levels specified in the argument
          'conf'. The last two columns are the sample size and the
          p-value of the test that "D'" is equal to zero.

     "r": a matrix with $m$ rows and $3+p$ columns, where $m$ is the
          number of markers in the geneSet, $p$ is the number of
          elements of the argument 'conf'. The first column is the
          estimated "r". The next $p$ columns are estimated confidence
          limits for the confidence levels specified in the argument
          'conf'. The last two columns are the sample size and the
          p-value of the test that "r" is equal to zero.

 "X$^2$": a matrix with $m$ rows and $3+p$ columns, where $m$ is the
          number of markers in the geneSet, $p$ is the number of
          elements of the argument 'conf'. The first column is the test
          statistic "X$^2$" for HWE test. The next $p$ columns are
          zeros. The last two columns are the sample size and the
          p-value of the test for Hardy-Weinberg equilibrium.

_A_u_t_h_o_r(_s):

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

_E_x_a_m_p_l_e_s:

     library(GeneticsBase)
     data(CAMP)

     HWE(CAMP)

