HWE.exact            package:GeneticsBase            R Documentation

_E_x_a_c_t _t_e_s_t _f_o_r _H_a_r_d_y-_W_e_i_n_b_e_r_g _E_q_u_i_l_i_b_r_i_u_m _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:

     Exact test for Hardy-Weinberg Equilibrium for a biallelic locus.

_U_s_a_g_e:

     HWE.exact(object, 
               marker, 
               founderOnly=TRUE)

_A_r_g_u_m_e_n_t_s:

  object: a geneSet object.

  marker: marker name for the biallelic locus.

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

_V_a_l_u_e:

     The function 'HWE' returns a list with class 'htest' containing
     the following elements: 

statistic: A 3-element vector records the genotype frequencies: 'N11',
          'N12', 'N22'.

parameter: A 2-element vector records the allele frequencies: 'N1' and
          'N2'

 p.value: p-value of the test.

  method: Information indicates if 'chisquare' method or 'exact' method
          is used to do HWE test.

data.name: name of the data set

observed: a table lists allele levels, allele pairs, and allele codes

_N_o_t_e:

     This function only works for genotypes with exactly 2 alleles.

_A_u_t_h_o_r(_s):

     David Duffy davidD@qimr.edu.au with modifications by Gregory R.
     Warnes, and Nitin Jain

_R_e_f_e_r_e_n_c_e_s:

     Emigh TH. (1980) "Comparison of tests for Hardy-Weinberg
     Equilibrium", Biometrics, 36, 627-642.

_S_e_e _A_l_s_o:

     'HWE.chisq'

_E_x_a_m_p_l_e_s:

     library(GeneticsBase)
     data(CAMP)

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

