xcmsEIC-class              package:xcms              R Documentation

_C_l_a_s_s _x_c_m_s_E_I_C, _a _c_l_a_s_s _f_o_r _m_u_l_t_i-_s_a_m_p_l_e _e_x_t_r_a_c_t_e_d _i_o_n _c_h_r_o_m_a_t_o_g_r_a_m_s

_D_e_s_c_r_i_p_t_i_o_n:

     This class is used to store and plot parallel extracted ion
     chromatograms from multiple sample files. It integrates with the
     'xcmsSet' class to display peak area integrated during peak
     identification or fill-in.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created with the 'getEIC' method of the 'xcmsSet'
     class. Objects can also be created by calls of the form
     'new("xcmsEIC", ...)'.

_S_l_o_t_s:

     '_e_i_c': list containing named entries for every sample. for each
          entry, a  list of two column EIC matricies with retention
          time and intensity

     '_m_z_r_a_n_g_e': two column matrix containing starting and ending m/z
          for each EIC

     '_r_t_r_a_n_g_e': two column matrix containing starting and ending time
          for each EIC

     '_r_t': either '"raw"' or '"corrected"' to specify retention times
          contained in the object

     '_g_r_o_u_p_n_a_m_e_s': group names from 'xcmsSet' object used to generate
          EICs

_M_e_t_h_o_d_s:

     _g_r_o_u_p_n_a_m_e_s 'signature(object = "xcmsEIC")': get 'groupnames' slot

     _m_z_r_a_n_g_e 'signature(object = "xcmsEIC")': get 'mzrange' slot

     _p_l_o_t 'signature(x = "xcmsEIC")': plot the extracted ion
          chromatograms

     _r_t_r_a_n_g_e 'signature(object = "xcmsEIC")': get 'rtrange' slot

     _s_a_m_p_n_a_m_e_s 'signature(object = "xcmsEIC")': get sample names

_N_o_t_e:

     No notes yet.

_A_u_t_h_o_r(_s):

     Colin A. Smith, csmith@scripps.edu

_S_e_e _A_l_s_o:

     'getEIC'

