c2bat                 package:pbatR                 R Documentation

_C_2_B_A_T

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

     C2BAT (c) Matt McQueen, Jessica Su, Christoph Lange.

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

     c2bat( snps,
            case.aa, case.Aa, case.AA,
            control.aa, control.Aa, control.AA,
            replicates=0,
            statistic="armitage",
            method="exact" )

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

    snps: Names of the snps (vector). Can be strings.

 case.aa: Number of cases with aa genotype (a vector corresponding to
          the snps).

 case.Aa: Number of cases with Aa genotype.

 case.AA: Number of cases with AA genotype.

control.aa: Number of controls with aa genotype.

control.Aa: Number of controls with Aa genotype.

control.AA: Number of controls with AA genotype.

replicates: This value should be set to zero for the first analysis.
          Then, once the top snps have been selected, this should be
          rerun with replicates>1000 for those selected snps.

statistic: '"armitage"' = the Armitage trend test. '"logrank"' =
          logrank test 

  method: '"exact"' = exact likelihood function '"approximate"' =
          approximate likelihood function 

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

     The output is formatted as follows: SNP, case.aa, case.Aa,
     case.AA, control.aa, control.Aa, control.AA, Monte-Carlo p-value,
     p-value, non-centrality parameter (for power calculations),
     modelc2-based OR, allelic OR.

     Note that the non-centrality parameter and the ORs are independent
     of the pvalues.

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

     ## Not run: 
     c2bat( snps=c("snp1","snp2"),
            case.aa=c(10,11), case.Aa=c(30,31), case.AA=c(14,44),
            control.aa=c(33,32), control.Aa=c(100,99), control.AA=c(0,0) )
     ## End(Not run)

