Armitage            package:GeneticsBase            R Documentation

_C_o_c_h_r_a_n-_A_r_m_i_t_a_g_e _t_e_s_t _f_o_r _l_i_n_e_a_r _t_r_e_n_d_s _i_n _p_r_o_p_o_r_t_i_o_n_s _a_n_d _f_r_e_q_u_e_n_c_i_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Cochran-Armitage test for linear trends in proportions and
     frequencies.

_U_s_a_g_e:

     Armitage(geneSetObj, method="A")
     Armitage.default(pedObj, method="A")
     ArmitageTest(x, mem)

_A_r_g_u_m_e_n_t_s:

geneSetObj: a geneSet object

  pedObj: a pedigree object

  method: genotype coding method. The default is additive coding ('A').
          The other two available coding methods are recessive coding
          ('R') and dominant coding ('D'), respectively.

       x: a vector of bialleleic markers coded by additive, recessive,
          or dominant model. Denote B as common allele and A as minor
          allele.

     _a_d_d_i_t_i_v_e _m_o_d_e_l: x=0 - BB; x=1 - AB; x=2 - AA

     _r_e_c_e_s_s_i_v_e _m_o_d_e_l: x=0 - BB; x=0 - AB; x=2 - AA

     _d_o_m_i_n_a_n_t _m_o_d_e_l: x=0 - BB; x=1 - AB; x=1 - AA 

     mem: disease membership. '1' - case; '0' - control

_V_a_l_u_e:

     The functions 'Armitage' and 'Armitage.default' return a matrix
     with 'nMarkers' rows and 2 columns, where 'nMarkers' is the number
     of markers. The two columns are test statistic ('stat') and
     p-value ('pvalue'), respectively.

     The function 'ArmitageTest' returns a list of two elements: 

   stat : test statistic

 pvalue : p-value of the test

_N_o_t_e:

     This implementation is based on the documentation at webpage:
     <URL:
     http://linkage.rockefeller.edu/pawe3d/help/Linear-trend-test-ncp.html>.

_A_u_t_h_o_r(_s):

     Gregory Warnes <warnes@bst.rochester.edu> Ross Lazarus
     <ross.lazarus@channing.harvard.edu> Weiliang Qiu
     <stwxq@channing.harvard.edu>

_R_e_f_e_r_e_n_c_e_s:

     Gordon D, Haynes C, Blumenfeld J, Finch SJ (2005)  PAWE-3D:
     visualizing Power for Association With Error in case/control 
     genetic studies of complex traits.  Bioinformatics 21:3935-3937.

     Gordon D, Finch SJ, Nothnagel M, Ott J (2002)  Power and sample
     size calculations for case-control genetic association  tests when
     errors are present: application to single nucleotide 
     polymorphisms.  Hum Hered 54:22-33.

     Chapman, D.G. and Nam, J.M. (1968)  Asymptotic power of chi square
     tests for linear trends in proportions.  Biometrics. 24, 315-327.

     Armitage, P. (1955)  Tests for linear trends in proportions and
     frequencies.  Biometrics. 11, 375-386.

     Cochran, W.G. (1954)  Some methods for strengthening the common
     chi-squared tests.  Biometrics. 10, 417-451.

_E_x_a_m_p_l_e_s:

       # not significant result
       ArmitageTest(x=c(2,1,1,1,0,0,1,0,0,1), mem=c(1,1,1,1,1,0,0,0,0,0))

       # significant result
       ArmitageTest(x=c(2,2,1,1,0,0,0,0,0,0), mem=c(1,1,1,1,1,0,0,0,0,0))

