findPeaks-methods            package:xcms            R Documentation

_F_e_a_t_u_r_e _d_e_t_e_c_t_i_o_n _f_o_r _G_C/_M_S _a_n_d _L_C/_M_S _D_a_t_a - _m_e_t_h_o_d_s

_D_e_s_c_r_i_p_t_i_o_n:

     A number of peak pickers exist in XCMS. 'findPeaks' is the generic
     method.

_A_r_g_u_m_e_n_t_s:

  object: 'xcmsRaw-class' object

  method: Method to use for peak detection. See details.

     ...: Optional arguments to be passed along

_D_e_t_a_i_l_s:

     Different algorithms can be used by specifying them with the
     'method' argument. For example to use the matched filter approach
     described by Smith et al (2006) one would use: 'findPeaks(object,
     method="matchedFilter")'. This is also the default.

     Further arguments given by '...' are passed through to the
     function implementing the 'method'. 

     A character vector of _nicknames_ for the  algorithms available is
     returned by  'getOption("BioC")$xcms$findPeaks.methods'. If the
     nickname of a method is called "centWave", the help page for that
     specific method can be accessed with '?findPeaks.centWave'.

_V_a_l_u_e:

     A matrix with columns: 

      mz: weighted (by intensity) mean of peak m/z across scans 

   mzmin: m/z of minimum step 

   mzmax: m/z of maximum step 

      rt: retention time of peak midpoint 

   rtmin: leading edge of peak retention time 

   rtmax: trailing edge of peak retention time 

    into: integrated area of original (raw) peak 

    maxo: maximum intensity of original (raw) peak 


     and additional columns depending on the choosen method.

_M_e_t_h_o_d_s:


     _o_b_j_e_c_t = "_x_c_m_s_R_a_w" ' findPeaks(object, ...) '


_S_e_e _A_l_s_o:

     'findPeaks.matchedFilter' 'findPeaks.centWave' 'xcmsRaw-class'

