annotate               package:CAMERA               R Documentation

_D_e_c_o_n_v_o_l_u_t_e/_A_n_n_o_t_a_t_e _L_C/_E_S_I-_M_S _d_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     Annotate isotope peaks, adducts and fragments for a (grouped)
     xcmsSet 'xs'. Returns a xsAnnotate object.

_U_s_a_g_e:

     annotate(xs, sigma = 6, perfwhm = 0.6, cor_eic_th = 0.75, maxcharge = 3, maxiso = 4, ppm = 5, mzabs = 0.01, multiplier = 3, sample=1, category = NA, polarity="positive")

_A_r_g_u_m_e_n_t_s:

      xs: xcmsSet with peak group assignments

   sigma: Isotopic peak relationship table

 perfwhm: Adduct/Fragment peak relationship table

cor_eic_th: correlation threshold (0..1)

maxcharge: max charge of the ions

  maxiso: max number of isotopes

     ppm: ppm error

   mzabs: absolut error

multiplier: max. number n of [nM+x] clusterions

  sample: Index of which sample is used for the correlation

category: Which class label should be used

polarity: Which polarity mode was used for measuring of the ms sample

_D_e_t_a_i_l_s:

     Batch script for a annotation for a a (grouped) xcmsSet 'xs'.
     Generate intern a xsAnnotate object and calls the member function
     for the annotation step. Returns a peaklist with additonal columns
     for isotopes, adducts and an index for the pseudo spectra group.
     xsAnnotate groups Peaks into spectra groups, after there
     Retentiontime and EIC correlations. Attention: For the EIC
     correlation only one sample can be used, so if the xcmsSet
     contains more than one sample, one must be chosen.

_V_a_l_u_e:

     'annotate' returns an xsAnnotate object. For more information
     about see xsAnnotate-class

_A_u_t_h_o_r(_s):

     Carsten Kuhl <ckuhl@ipb-halle.de>

_E_x_a_m_p_l_e_s:

      library(CAMERA)
      file <- system.file('mzdata/MM14.mzdata', package = "CAMERA")
      xs   <- xcmsSet(file, method="centWave", ppm=30, peakwidth=c(5,10))
      annotated_xs<- annotate(xs)

