getPeaks               package:PROcess               R Documentation

_P_e_a_k _D_e_t_e_c_t_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     For given threshold criteria, find peaks.

_U_s_a_g_e:

     getPeaks(bseoffM, peakinfofile,SoN = 2,span = 81,sm.span=11, 
     zerothrsh=2, area.w = 0.003, ratio = 0.2)

_A_r_g_u_m_e_n_t_s:

 bseoffM: a matrix holding the baseline-substracted spectra, with 
          row-names as the m/z values and column-names  as the spectrum
          names.

peakinfofile: a `.csv' file in the same format as   Ciphergen's peak
          info file, with 5 columns  data.  More details later.

     SoN: see isPeak().

    span: see isPeak().

 sm.span: see isPeak().

zerothrsh: ignore peaks whose intensity values are below zerothrsh.

  area.w: see isPeak().

   ratio: see isPeak().

_D_e_t_a_i_l_s:

     For given threshold criteria, detect peaks and write the 
     following columns of information into 'peakinfofile',  spectrum
     name (Spectrum.Tag), spectrum sequential number (Spectrum.), peak
     sequential number within a spectrum (Peak.), relative intensity
     (Intensity) and the m/z value where the  relative intensity occurs
     (Substance.Mass).

_A_u_t_h_o_r(_s):

     Xiaochun Li

_S_e_e _A_l_s_o:

     'rmBaseline'

_E_x_a_m_p_l_e_s:

     example(renorm)
     peakfile <- paste(tempdir(),"testpeakinfo.csv", sep="/")
     getPeaks(rtM, peakfile)

