parseChromaTOF            package:flagme            R Documentation

_P_a_r_s_e_r _f_o_r _C_h_r_o_m_a_T_O_F _f_i_l_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Reads ASCII ChromaTOF-format files from AMDIS (Automated Mass
     Spectral Deconvolution and Identification System)

_U_s_a_g_e:

     parseChromaTOF(fn,min.pc=.01,mz=seq(85,500),rt.cut=.008,rtrange=NULL,skip=1,rtDivide=60)

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

      fn: ChromaTOF filename to read.

  min.pc: minimum percent of maximum intensity.

      mz: vector of mass-to-charge bins of raw data table.

  rt.cut: the difference in retention time, below which peaks are
          merged together.

 rtrange: retention time range to parse peaks from, can speed up
          parsing if only interested in a small region (must be
          'numeric' vector of length 2)

    skip: number of rows to skip at beginning of the ChromaTOF

rtDivide: multiplier to divide the retention times by (default: 60)

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

     'parseChromaTOF' will typically be called by 'addChromaTOFPeaks',
     not called directly.

     Peaks that are detected within 'rt.cut' are merged together.  This
     avoids peaks which are essentially overlapping.

     Fragments that are less than 'min.pc' of the maximum intensity
     fragment are discarded.

_V_a_l_u_e:

     'list' with components 'peaks' (table of spectra - rows are
     mass-to-charge and columns are the  different detected peaks) and
     'tab' (table of features for each detection), according to what is
     stored in  the ChromaTOF file.

_A_u_t_h_o_r(_s):

     Mark Robinson

_R_e_f_e_r_e_n_c_e_s:

     Mark D Robinson (2008).  Methods for the analysis of gas
     chromatography - mass spectrometry data  _PhD dissertation_
     University of Melbourne.

_S_e_e _A_l_s_o:

     'addAMDISPeaks'

_E_x_a_m_p_l_e_s:

     require(gcspikelite)

     # paths and files
     gcmsPath<-paste(.find.package("gcspikelite"),"data",sep="/")
     tofFiles<-dir(gcmsPath,"tof",full=TRUE)

     # parse ChromaTOF file
     cTofList<-parseChromaTOF(tofFiles[1])

