quality               package:PROcess               R Documentation

_Q_u_a_l_i_t_y _C_h_e_c_k _o_n _a _S_e_t _o_f _S_p_e_c_t_r_a

_D_e_s_c_r_i_p_t_i_o_n:

     Compute three quality parameters for a set of spectra.

_U_s_a_g_e:

     quality(Ma, peakinfofile, cutoff)

_A_r_g_u_m_e_n_t_s:

      Ma: a Matrix where the baseline-subtracted spectra are stored
          column wise.

peakinfofile: a `.csv' file in the same format as  Ciphergen's peak
          info file, with 5 columns data. See Details of 'getPeaks'.

  cutoff: The point in m/z below which spectra are cutoff.

_D_e_t_a_i_l_s:

     The quality parameters are computed a la fashion de Mani. 1.
     Estimate noise by moving average with a 5 point window. 2.
     Estimate the noise envelop by 3 times the standard deviation of
     noise in a 251 point moving window. 3. Compute the area under the
     baseline-subtracted curve, area0. 4. Compute the area after
     subtracting the noise envelop from the baseline-subtracted curve,
     area1. 5. Parameter 'Quality' is defined as area1/area0. 6.
     Parameter 'Retain' is defined as the number of points with height
     above 5 times the noise envelop over total number of points in the
     spectrum. 7. Detect peaks in each spectrum by 'getPeaks' or
     Ciphergen software. 8. Parameter 'peak' is defined as the number
     of peaks in a spectrum divided by the mean number of peaks across
     spectra.

     A spectrum is considered to be of poor quality if Quality<0.4,
     Retain<0.1 and peak<0.5 simultaneously.

_V_a_l_u_e:

     A matrix with three named columns, 'Quality','Retain' and 'peak',
     with spectrum file names as row names.

_A_u_t_h_o_r(_s):

     Xiaochun Li

_E_x_a_m_p_l_e_s:

     example(getPeaks)
     qualRes <- quality(testM, peakfile, cutoff=1500)

