exactTestNB              package:edgeR              R Documentation

_A_n _e_x_a_c_t _t_e_s_t _f_o_r _d_i_f_f_e_r_e_n_c_e_s _b_e_t_w_e_e_n _t_w_o _n_e_g_a_t_i_v_e _b_i_n_o_m_i_a_l _g_r_o_u_p_s

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

     An exact test for differences between two negative binomial groups

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

      
     exactTestNB(pseudo, group, pair=1:2, mus, r, verbose=TRUE)

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

  pseudo: data (e.g. quantile adjusted pseudodata) on which to compute
          Fisher exact statistics

   group: group indicator, must be same length as ncol(pseudo)

    pair: pair of groups to be compared

     mus: vector of means under the null hypothesis (of no difference
          between groups)

       r: preset or estimated negative binomial 'size' parameter.  If
          you want to run a Poisson test, set r very large (e.g. 1000)

 verbose: whether to write comments, default 'TRUE'

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

     vector of p-values

_A_u_t_h_o_r(_s):

     Mark Robinson, Davis McCarthy

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

     y<-matrix(rnbinom(20,mu=10,size=1.5),nrow=5)
     group<-factor(c(1,1,2,2))
     mus<-rep(10,5)
     f<-exactTestNB(y,group,pair=c(1,2),mus,r=1.5)

