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'

