xcmsSet-class              package:xcms              R Documentation

_C_l_a_s_s _x_c_m_s_S_e_t, _a _c_l_a_s_s _f_o_r _p_r_e_p_r_o_c_e_s_s_i_n_g _p_e_a_k _d_a_t_a

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

     This class transforms a set of peaks from multiple LC/MS or GC/MS
     samples into a matrix of preprocessed data. It groups the peaks
     and does nonlinear retention time correction without internal
     standards. It fills in missing peak values from raw data. Lastly,
     it generates extracted ion chromatograms for ions of interest.

_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 'xcmsSet' constructor which
     gathers peaks from a set NetCDF files. Objects can also be created
     by calls of the form 'new("xcmsSet", ...)'.

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


     '_p_e_a_k_s': matrix containing peak data

     '_g_r_o_u_p_s': matrix containing statistics about peak groups

     '_g_r_o_u_p_i_d_x': list containing indices of peaks in each group

     '_s_a_m_p_n_a_m_e_s': character vector with names of each sample

     '_s_a_m_p_c_l_a_s_s': factor containing sample classes

     '_r_t': list containing two lists, 'raw' and 'corrected', each
          containing retention times for every scan of every sample

     '_c_d_f_p_a_t_h_s': character vector with absolute path name of each
          NetCDF file

     '_p_r_o_f_i_n_f_o': list containing two values, 'method' - profile
          generation method, and 'step' - profile m/z step size


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


     _c 'signature("xcmsSet")': combine objects together

     _c_d_f_p_a_t_h_s<- 'signature(object = "xcmsSet")': set 'cdfpaths' slot

     _c_d_f_p_a_t_h_s 'signature(object = "xcmsSet")': get 'cdfpaths' slot

     _d_i_f_f_r_e_p_o_r_t 'signature(object = "xcmsSet")': create report of
          differentially regulated ions including EICs

     _f_i_l_l_P_e_a_k_s 'signature(object = "xcmsSet")': fill in peak data for
          groups with missing peaks

     _g_e_t_E_I_C 'signature(object = "xcmsSet")': get list of EICs for each
          sample in the set

     _g_r_o_u_p_i_d_x<- 'signature(object = "xcmsSet")': set 'groupidx' slot

     _g_r_o_u_p_i_d_x 'signature(object = "xcmsSet")': get 'groupidx' slot

     _g_r_o_u_p_n_a_m_e_s 'signature(object = "xcmsSet")': get textual names for
          peak groups

     _g_r_o_u_p_s<- 'signature(object = "xcmsSet")': set 'groups' slot

     _g_r_o_u_p_s 'signature(object = "xcmsSet")': get 'groups' slot

     _g_r_o_u_p_v_a_l 'signature(object = "xcmsSet")': get matrix of values
          from peak data with a row for each peak group

     _g_r_o_u_p 'signature(object = "xcmsSet")': find groups of peaks across
          samples that share similar m/z and retention times

     _p_e_a_k_s<- 'signature(object = "xcmsSet")': set 'peaks' slot

     _p_e_a_k_s 'signature(object = "xcmsSet")': get 'peaks' slot

     _p_l_o_t_r_t 'signature(object = "xcmsSet")': plot retention time
          deviation profiles

     _p_r_o_f_i_n_f_o<- 'signature(object = "xcmsSet")': set 'profinfo' slot

     _p_r_o_f_i_n_f_o 'signature(object = "xcmsSet")': get 'profinfo' slot

     _r_e_t_c_o_r 'signature(object = "xcmsSet")': use initial grouping of
          peaks to do nonlinear loess retention time correction

     _s_a_m_p_c_l_a_s_s<- 'signature(object = "xcmsSet")': set 'sampclass' slot

     _s_a_m_p_c_l_a_s_s 'signature(object = "xcmsSet")': get 'sampclass' slot

     _s_a_m_p_n_a_m_e_s<- 'signature(object = "xcmsSet")': set 'sampnames' slot

     _s_a_m_p_n_a_m_e_s 'signature(object = "xcmsSet")': get 'sampnames' slot

     _s_p_l_i_t 'signature("xcmsSet")': divide into a list of objects


_N_o_t_e:

     No notes yet.

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

     Colin A. Smith, csmith@scripps.edu

_R_e_f_e_r_e_n_c_e_s:

     A parallel effort in metabolite profiling data sharing: <URL:
     http://metlin.scripps.edu/>

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

     'xcmsSet'

