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(y1, y2, lib.size1, lib.size2, r, tol = 1e-10, maxit = 30) 

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

      y1: matrix of counts for first group

      y2: matrix of counts for second group

lib.size1: vector of library sizes for first group

lib.size2: vector of library sizes for second group

       r: size parameter of negative binomial

     tol: tolerance between iterations

   maxit: maximum number of iterations

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

     list with elements 'p' (overall proportion), 'p1' (estimates for
     first group), 'p2' (estimates for second group)

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

     Mark Robinson

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

     y1<-matrix(rnbinom(10,size=1,mu=10),nrow=5)
     y2<-matrix(rnbinom(10,size=1,mu=5),nrow=5)
     ps<-estimatePs(y1,y2,c(1000,1001),c(1000,1001),r=1)

