xcmsRaw-class              package:xcms              R Documentation

_C_l_a_s_s _x_c_m_s_R_a_w, _a _c_l_a_s_s _f_o_r _h_a_n_d_l_i_n_g _r_a_w _d_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     This class handles processing and visualization of the raw data
     from a single LC/MS or GS/MS run. It includes methods for
     producing a standard suite of plots including individual spectra,
     multi-scan average spectra, TIC, and EIC. It will also produce a
     feature list of significant peaks using matched filtration.

_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 'xcmsRaw' constructor which reads
     data from a NetCDF file into a new object.

_S_l_o_t_s:


     '_e_n_v': environment with three variables: 'mz' - concatenated m/z
          values for all scans, 'intensity' - corresponding signal
          intensity for each m/z value, and 'profile' - matrix
          represention of the intensity values with columns
          representing scans and rows representing equally spaced m/z
          values

     '_t_i_c': numeric vector with total ion count (intensity) for each
          scan

     '_s_c_a_n_t_i_m_e': numeric vector with acquisition time (in seconds) for
          each scan

     '_s_c_a_n_i_n_d_e_x': integer vector with starting positions of each scan
          in the 'mz' and 'intensity' variables (note that index values
          are based off a 0 initial position instead of 1)

     '_p_r_o_f_m_e_t_h_o_d': characer value with name of method used for
          generating the profile matrix

     '_m_z_r_a_n_g_e': numeric vector of length 2 with minimum and maximum m/z
          values represented in the profile matrix

     '_g_r_a_d_i_e_n_t': matrix with first row, 'time', containing the time
          point for interpolation and successive columns representing
          solvent fractions at each point

     '_m_s_m_s_i_n_f_o': matrix with first row, 'parent', containing parent ion
          m/z and sucessive columns representing additional information
          about fragmentation (energy, etc.)


_M_e_t_h_o_d_s:


     _f_i_n_d_P_e_a_k_s 'signature(object = "xcmsRaw")': feature detection using
          matched filtration in the chromatographic time domain

     _g_e_t_E_I_C 'signature(object = "xcmsRaw")': get extracted ion
          chromatograms in specified m/z ranges

     _g_e_t_P_e_a_k_s 'signature(object = "xcmsRaw")': get data for peaks in
          specified m/z and time ranges

     _g_e_t_S_c_a_n 'signature(object = "xcmsRaw")': get m/z and intensity
          values for a single mass scan

     _g_e_t_S_p_e_c 'signature(object = "xcmsRaw")': get average m/z and
          intensity values for multiple mass scans

     _i_m_a_g_e 'signature(x = "xcmsRaw")': get data for peaks in specified
          m/z and time ranges

     _p_l_o_t_C_h_r_o_m 'signature(object = "xcmsRaw")': plot a chromatogram
          from profile data

     _p_l_o_t_R_a_w 'signature(object = "xcmsRaw")': plot locations of raw
          intensity data points

     _p_l_o_t_S_c_a_n 'signature(object = "xcmsRaw")': plot a mass spectrum of
          an individual scan from the raw data

     _p_l_o_t_S_p_e_c 'signature(object = "xcmsRaw")': plot a mass spectrum
          from profile data

     _p_l_o_t_S_u_r_f 'signature(object = "xcmsRaw")': experimental method for
          plotting 3D surface of profile data with 'rgl'.

     _p_l_o_t_T_I_C 'signature(object = "xcmsRaw")': plot total ion count
          chromatogram

     _p_r_o_f_M_e_d_F_i_l_t 'signature(object = "xcmsRaw")': median filter profile
          data in time and m/z dimensions

     _p_r_o_f_M_e_t_h_o_d<- 'signature(object = "xcmsRaw")': change the method of
          generating the 'profile' matrix

     _p_r_o_f_M_e_t_h_o_d 'signature(object = "xcmsRaw")': get the method of
          generating the 'profile' matrix

     _p_r_o_f_M_z 'signature(object = "xcmsRaw")': get vector of m/z values
          for each row of the 'profile' matrix

     _p_r_o_f_R_a_n_g_e 'signature(object = "xcmsRaw")': interpret flexible ways
          of specifying subsets of the 'profile' matrix

     _p_r_o_f_S_t_e_p<- 'signature(object = "xcmsRaw")': change the m/z step
          used for generating the 'profile' matrix

     _p_r_o_f_S_t_e_p 'signature(object = "xcmsRaw")': get the m/z step used
          for generating the 'profile' matrix

     _r_e_v_M_z 'signature(object = "xcmsRaw")': reverse the order of the
          data points for each scan

     _s_o_r_t_M_z 'signature(object = "xcmsRaw")': sort the data points by
          increasing m/z for each scan


_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:

     'xcmsRaw'

