removeIndex            package:altcdfenvs            R Documentation

_A _f_u_n_c_t_i_o_n _t_o _r_e_m_o_v_e _p_r_o_b_e_s _i_n _a_n _e_n_v_i_r_o_n_m_e_n_t

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

     A function to remove probes in an environment, given their index.

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

     removeIndex(x, i, simplify = TRUE, verbose = FALSE)

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

       x: An instance of 'CdfEnvAffy-class' 

       i: A vector of indexes (integers !). 

simplify: Simply the resulting 'CdfEnvAffy' (see details). 

 verbose: verbose output or not. 

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

     The probes to be removed are set to 'NA' in the CdfEnvAffy. When
     'simplify' is set to 'TRUE' the probe sets are simplified whenever
     possible. For example, if both pm and mm for the same probe pair
     are set to 'NA', then the probe pair is removed from the probe
     set.

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

     An instance of 'CdfEnvAffy-class' is returned.

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

     Laurent Gautier

_S_e_e _A_l_s_o:

     'CdfEnvAffy-class'

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

     ## use plasmodiumanopheles chip as an example
     if (require(plasmodiumanophelescdf)) {

       ## wrap in a (convenient) CdfEnvAffy object
       planocdf <- wrapCdfEnvAffy(plasmodiumanophelescdf, 712, 712, "plasmodiumanophelescdf")
       print(planocdf)

       ## ask for the probe indexed '10759' to be removed
       ## (note: if one wishes to remove from X/Y coordinates,
       ## the function xy2index can be of help).
       planocdfCustom <- removeIndex(planocdf, as.integer(10759))

       ## let see what happened (we made this example knowing in which
       ## probe set the probe indexed '10759' is found).
       indexProbes(planocdf, "pm", "200000_s_at")
       indexProbes(planocdfCustom, "pm", "200000_s_at")
       ## The 'second' pm probe (indexed '10579') in the probe set is now set
       ## to NA.
     }

