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

     '_p_h_e_n_o_D_a_t_a': a data frame containing the experimental design
          factors

     '_r_t': list containing two lists, 'raw' and 'corrected', each
          containing retention times for every scan of every sample

     '_f_i_l_e_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

     _f_i_l_e_p_a_t_h_s<- 'signature(object = "xcmsSet")': set 'filepaths' slot

     _f_i_l_e_p_a_t_h_s 'signature(object = "xcmsSet")': get 'filepaths' 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")': *DEPRECATED*. If
          used, the experimental design will be replaced with a data
          frame with a single column matching the supplied factor.

     _s_a_m_p_c_l_a_s_s 'signature(object = "xcmsSet")': get the interaction of
          the experimental design factors

     _p_h_e_n_o_D_a_t_a<- 'signature(object = "xcmsSet")': set the 'phenoData'
          slot

     _p_h_e_n_o_D_a_t_a 'signature(object = "xcmsSet")': set the 'phenoData'
          slot

     _s_a_m_p_n_a_m_e_s<- 'signature(object = "xcmsSet")': set rownames in the
          'phenoData' slot

     _s_a_m_p_n_a_m_e_s 'signature(object = "xcmsSet")': get rownames in the
          'phenoData' 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'

