xcmsRaw                 package:xcms                 R Documentation

_C_o_n_s_t_r_u_c_t_o_r _f_o_r _x_c_m_s_R_a_w _o_b_j_e_c_t_s _w_h_i_c_h _r_e_a_d_s _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 task of reading a NetCDF/mzXML file
     containing LC/MS or GC/MS data into a new 'xcmsRaw' object. It
     also transforms the data into profile (maxrix) mode for efficient
     plotting and data exploration.

_U_s_a_g_e:

     xcmsRaw(filename, profstep = 1, profmethod = "intlin", profparam =
     list(), includeMSn=FALSE)

_A_r_g_u_m_e_n_t_s:

filename: path name of the NetCDF or mzXML file to read

profstep: step size (in m/z) to use for profile generation

profmethod: method to use for profile generation

profparam: extra parameters to use for profile generation

includeMSn: only for XML file formats: also read MS$^n$ (Tandem-MS of
          Ion-/Orbi- Trap spectra)

_D_e_t_a_i_l_s:

     If 'profstep' is set to 0, no profile matrix is generated. Unless
     includeMSn=TRUE only first level MS data is read, not MS/MS, etc.)

_V_a_l_u_e:

     A 'xcmsRaw' object.

_A_u_t_h_o_r(_s):

     Colin A. Smith, csmith@scripps.edu

_R_e_f_e_r_e_n_c_e_s:

     NetCDF file format: <URL:
     http://my.unidata.ucar.edu/content/software/netcdf/> <URL:
     http://www.astm.org/Standards/E2077.htm> <URL:
     http://www.astm.org/Standards/E2078.htm>

     mzXML file format: <URL:
     http://sashimi.sourceforge.net/software_glossolalia.html>

     PSI-MS working group who developed mzData and mzML file formats:
     <URL: http://www.psidev.info/index.php?q=node/80>

     Parser used for XML file formats: <URL:
     http://tools.proteomecenter.org/wiki/index.php?title=Software:RAMP>

_S_e_e _A_l_s_o:

     'xcmsRaw-class', 'profStep', 'profMethod' 'xcmsFragments'

