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 _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 = list.files(pattern = ".[Cc][Dd][Ff]$", recursive = TRUE), 
             snames = gsub(".[^.]*$", "", basename(files)), 
             sclass = gsub("^.$", "sample", dirname(files)), profmethod = "bin",
             profparam = list(), ...)

_A_r_g_u_m_e_n_t_s:

   files: path names of the NetCDF files to read

  snames: sample names

  sclass: sample classes

profmethod: method to use for profile generation

profparam: parameters to use for profile generation

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

_D_e_t_a_i_l_s:

     The default values of the 'files', 'snames', and 'sclass'
     arguments cause the function to recursively search for *.cdf
     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.

_N_o_t_e:

_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'

