groupval-methods            package:xcms            R Documentation

_E_x_t_r_a_c_t _a _m_a_t_r_i_x _o_f _p_e_a_k _v_a_l_u_e_s _f_o_r _e_a_c_h _g_r_o_u_p

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

     Generate a matrix of peak values with rows for every group and
     columns for every sample. The value included in the matrix can be
     any of the columns from the 'xcmsSet' 'peaks' slot matrix.
     Collisions where more than one peak from a single sample are in
     the same group get resolved with one of several user-selectable
     methods.

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

  object: the 'xcmsSet' object

  method: conflict resolution method, '"medret"' to use the peak
          closest to the median retention time or '"maxint"' to use the
          peak with the highest intensity 

   value: name of peak column to enter into returned matrix, or
          '"index"' for index to the corresponding row in the 'peaks'
          slot matrix 

intensity: if 'method == "maxint"', name of peak column to use for
          intensity 

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

     A matrix with with rows for every group and columns for every
     sample. Missing peaks have 'NA' values.

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


     _o_b_j_e_c_t = "_x_c_m_s_S_e_t" 'groupval(object, method = c("medret",
          "maxint"), value = "index", intensity = "into")'


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

     'xcmsSet-class'

