MCPDT                 package:MCPDT                 R Documentation

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_M_o_n_t_e _C_a_r_l_o _P_e_d_i_g_r_e_e _P_a_r_e_n_t_a_l-_A_s_y_m_m_e_t_r_y _T_e_s_t (_M_C_P_P_A_T)

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

     Pedigree disequilibrium test (PDT) and pedigree parental-asymmetry
     test (PPAT) with missing genotypes simulated conditioned on
     observed genotypes.

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

       MCPDT(ped,mcsize,loci=NULL,af=NULL,sexlinked=FALSE)

       MCPPAT(ped,mcsize,loci=NULL,af=NULL,sexlinked=FALSE)

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

     ped: name of a standard LINKAGE pedigree file (pre-makeped format)
          or a matrix/dataframe containing the pedigree data

  mcsize: Monte Carlo sample size

    loci: name of a standard LINKAGE loci file

      af: matrix of marker allele frequencies, one column for each
          marker

sexlinked: whether the markers are on X chromosome

_D_e_t_a_i_l_s:

     'MCPDT' calculates PDT and MCPDT statistics and p-values.

     'MCPPAT' calculates PDT, MCPDT, PPAT and MCPPAT statistics and
     p-values.

     ped is required. Only SNP markers are supported. If loci file is
     provided, allele frequencies are read from the file specified.
     Otherwise, they can be provided directly in the argument af. If
     allele frequencies are not provided in either way, they are
     estimated from all the typed founders' genotypes.

     If there are multiple markers, each marker is analyzed separately.

     sexlinked only applies to MCPDT since MCPPAT only deals with
     autosomal markers. If sexlinked=TRUE in 'MCPPAT', only PDT and
     MCPDT will be calculated.

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

   Tstat: PDT T statistics for the markers

  pvalue: P values assuming asymptotic normal distribution

  mcsize: Monte Carlo sample size

      af: allele frequencies used in the simulation

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

     Martin, E. R., Monks, S. A., Warren, L. L. and Kaplan, N. L.
     (2000) A test for linkage and association in general pedigrees:
     the pedigree disequilibrium test. Am J Hum Genet 67:146-154

     Ding, J., Lin, S. and Liu, Y. (2006) Monte Carlo pedigree
     disequilibrium test for markers on the X chromosome. Am J Hum
     Genet 79:567-573  

     Zhou, J.Y., Ding, J., Fung, W.K. and Lin, S. (2009) Detection of
     parent-of-origin effects using general pedigree data. Submitted

     Ott, J. (1989) Computer-simulation methods in human linkage
     analysis. Proc Natl Acad Sci USA 86:4175-4178

     Weeks, D. E., Ott, J., and Lathrop, G. M. (1990) SLINK: A general
     simulation program for linkage analysis. Am J Hum Genet 47:A204

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

