geneSubsets-class          package:Rmagpie          R Documentation

_g_e_n_e_S_u_b_s_e_t_s: _A _c_l_a_s_s _t_o _h_a_n_d_l_e _t_h_e _s_i_z_e_s _o_f _g_e_n_e _s_u_s_b_e_t_s _t_o _b_e _t_e_s_t_e_d _d_u_r_i_n_g _f_o_r_w_a_r_d _g_e_n_e _s_e_l_e_c_t_i_o_n

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

     Forward gene selection is usually a computationally expensive
     task. To reduce the computation expense one may want to do not
     consider one gene at a time but chunks of genes. This class store
     the sizes of gene susbets to be tested during forward gene
     selection.

_C_r_e_a_t_i_n_g _o_b_j_e_c_t_s:

     'new("geneSubsets", optionValues)'

     Create a geneSubsets, the sizes of the different subsets are
     determined by 'optionValues'. The size of the biggest subset
     'maxSubsetSize' and the number of subsets to be tried
     'noOfOptions' are automatically deducted. The speed is set to
     'high' is there are less models than the size of the biggest
     subset and 'slow' if not.

     'new("geneSubsets", maxSubsetSize, speed="high")'

     Create a geneSubsets, with a biggest subset of size
     'maxSubsetSize'. If the 'speed' is 'high' the sizes of the subsets
     are increased by a power of 2 from 1 to the biggest power of 2
     smaller than 'maxSubsetSize'. If the speed is 'slow' the sizes of
     the subsets are increased by 1 from 1 to the 'maxSubsetSize'.

_S_l_o_t_s:


     '_m_a_x_S_u_b_s_e_t_S_i_z_e': 'numeric'. Size of the biggest subset

     '_o_p_t_i_o_n_V_a_l_u_e_s': 'numeric' (vector). Sizes of the subsets in
          acsending order

     '_n_o_O_f_O_p_t_i_o_n_s': 'numeric'. Total number of subsets to be tried
          during backward gene selection

     '_s_p_e_e_d': 'character'. Speed of the backward feature selection.
          'high' if the number of models is smaller than the size of
          the biggest subset, 'slow' if not.

_M_e_t_h_o_d_s:


     '_g_e_t_M_a_x_S_u_b_s_e_t_S_i_z_e(_g_e_n_e_S_u_b_s_e_t_s), _g_e_t_M_a_x_S_u_b_s_e_t_S_i_z_e(_g_e_n_e_S_u_b_s_e_t_s)<-' 
          Retreive and modify the size of the biggest subset (slot
          maxSubsetSize)

     '_g_e_t_O_p_t_i_o_n_V_a_l_u_e_s(_g_e_n_e_S_u_b_s_e_t_s), _g_e_t_O_p_t_i_o_n_V_a_l_u_e_s(_g_e_n_e_S_u_b_s_e_t_s)<-' 
          Retreive and modify the sizes of the subsets of features
          (slot optionValues)

     '_g_e_t_N_o_O_f_O_p_t_i_o_n_s(_g_e_n_e_S_u_b_s_e_t_s)' Retreive the total number of subsets
          to be tried during backward gene selection (slot noModels)

     '_g_e_t_S_p_e_e_d(_g_e_n_e_S_u_b_s_e_t_s), _g_e_t_S_p_e_e_d(_g_e_n_e_S_u_b_s_e_t_s)<-' Retreive and
          modify the speed of the backward feature selection. (slot
          speed)

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

     Camille Maumet

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

     'thresholds','assessment'

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

     geneSubset235 <- new("geneSubsets", optionValues=c(2,3,5))
     geneSubset235
     getSubsetsSizes(geneSubset235)
     getSpeed(geneSubset235)
     getMaxSubsetSize(geneSubset235)

     geneSubsetMax60 <- new("geneSubsets", maxSubsetSize=60, speed="slow")
     geneSubsetMax60

     geneSubsetSlow <- new("geneSubsets", maxSubsetSize=70, speed="slow")
     geneSubsetSlow

     getMaxSubsetSize(geneSubsetMax60) <- 70
     geneSubsetMax60

     newSizes <- c(1,2,3,4,5)
     getSubsetsSizes(geneSubsetMax60) <- newSizes
     geneSubsetMax60

     getSpeed(geneSubset235) <- 'slow'
     geneSubset235

