estimatePs               package:edgeR               R Documentation

_E_s_t_i_m_a_t_e _e_x_p_r_e_s_s_i_o_n _p_r_o_p_o_r_t_i_o_n_s

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

     Estimate expression proportions (maximum likelihood with size
     fixed) based on negative binomial for each tag and sample group
     (only 2 groups implemented at this point)

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

      
     estimatePs(object, r, tol = 1e-10, maxit = 30) 

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

  object: list containing the raw data with elements 'data' (table of
          counts), 'group' (vector indicating group) and 'lib.size'
          (vector of library sizes)

       r: size parameter of negative binomial

     tol: tolerance between iterations

   maxit: maximum number of iterations

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

     list with elements 'p.common' (vector giving overall proportion
     for each tag), 'p.group' (matrix with columns giving estimates of
     proportions for different groups)

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

     Mark Robinson, Davis McCarthy

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

     set.seed(0)
     y<-matrix(rnbinom(40,size=1,mu=10),ncol=4)
     d<-DGEList(data=y,group=rep(1:2,each=2),lib.size=rep(c(1000:1001),2))
     ps<-estimatePs(d,r=1)

