xcmsSet                 package:xcms                 R Documentation

_C_o_n_s_t_r_u_c_t_o_r _f_o_r _x_c_m_s_S_e_t _o_b_j_e_c_t_s _w_h_i_c_h _f_i_n_d_s _p_e_a_k_s _i_n _N_e_t_C_D_F/_m_z_X_M_L _f_i_l_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     This function handles the construction of xcmsSet objects. It
     finds peaks in batch mode and pre-sorts files from subdirectories
     into different classes suitable for grouping.

_U_s_a_g_e:

     xcmsSet(files = NULL, snames = NULL, sclass = NULL, phenoData = NULL,
             profmethod = "bin", profparam = list(),
             polarity = NULL, nSlaves=0, ...)

_A_r_g_u_m_e_n_t_s:

   files: path names of the NetCDF/mzXML files to read

  snames: sample names

  sclass: sample classes

phenoData: sample names and classes

profmethod: method to use for profile generation

profparam: parameters to use for profile generation

polarity: filter raw data for positive/negative scans

 nSlaves: number of MPI-slaves to use for parallel peak detection,
          works only if 'Rmpi' is installed properly, see 'xcmsPapply'.

     ...: further arguments to the 'findPeaks' method of the 'xcmsRaw'
          class 

_D_e_t_a_i_l_s:

     The default values of the 'files', 'snames', 'sclass', and
     'phenoData' arguments cause the function to recursively search for
     readable files. The filename without extention is used for the
     sample name. The subdirectory path is used for the sample class.
     If the files contain both positive and negative spectra, the
     polarity can be selected explicitely. The default (NULL) is to
     read all scans.

_V_a_l_u_e:

     A 'xcmsSet' object.

_A_u_t_h_o_r(_s):

     Colin A. Smith, csmith@scripps.edu

_S_e_e _A_l_s_o:

     'xcmsSet-class', 'findPeaks', 'profStep', 'profMethod'

