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(), 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

 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.

_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'

