appendCdfEnvAffy         package:altcdfenvs         R Documentation

_a_p_p_e_n_d _p_r_o_b_e _s_e_t_s _t_o _a _C_d_f_E_n_v_A_f_f_y

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

     append probe sets to a CdfEnvAffy

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

     appendCdfEnvAffy(acdfenv, id, i, nocopy = TRUE)

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

 acdfenv: instance of class 'CdfEnvAffy'

      id: identifier for the probe set to add 

       i: a 'matrix' of indexes (see details)

  nocopy: whether to make a copy of the environment or not (see
          details)

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

     The 'matrix' 'i' must have one column per probe type. For typical
     Affymetrix chip types, there are two probe types: '"pm"' and
     '"mm"'.

     'nocopy' set to 'TRUE' means that the environment is added the
     probe set 'in-situ' (this can boost execution speed if you add a
     lot of probe sets).

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

     An 'CdfEnvAffy' is returned

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

     data(cdfenvEx)

     ## pm and mm probe set
     m <- matrix(1:10, ncol = 2)
     colnames(m) <- c("pm", "mm")

     appendCdfEnvAffy(cdfenvEx, "blabla", m)

     indexProbes(cdfenvEx, c("pm", "mm"), "blabla")

     ## pm only probe set
     m <- matrix(6:9, ncol = 1)
     colnames(m) <- c("pm")
     appendCdfEnvAffy(cdfenvEx, "blabla2", m)
     ## note that the unspecified "mm" were set to NA
     indexProbes(cdfenvEx, c("pm", "mm"), "blabla2")

