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'

