getEIC-methods             package:xcms             R Documentation

_G_e_t _e_x_t_r_a_c_t_e_d _i_o_n _c_h_r_o_m_a_t_o_g_r_a_m_s _f_o_r _s_p_e_c_i_f_i_e_d _m/_z _r_a_n_g_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Generate multiple extracted ion chromatograms for m/z values of
     interest.  For 'xcmsSet' objects, reread original raw data and
     apply precomputed retention time correction, if applicable.

_A_r_g_u_m_e_n_t_s:

  object: the 'xcmsRaw' or 'xcmsSet' object

 mzrange: either a two column matrix with minimum or maximum m/z or a
          matrix of any dimensions containing columns 'mzmin' and
          'mzmax'

          for 'xcmsSet' objects, if left blank the group data will be
          used instead 

 rtrange: a two column matrix the same size as 'mzrange' with minimum
          and maximum retention times between which to return EIC data
          points

          for 'xcmsSet' objects, it may also be a single number
          specifying the time window around the peak to return EIC data
          points 

    step: step size to use for profile generation

groupidx: either character vector with names or integer vector with
          indicies of peak groups for which to get EICs 

sampleidx: either character vector with names or integer vector with
          indicies of samples for which to get EICs 

      rt: '"corrected"' for using corrected retention times, or '"raw"'
          for using raw retention times 

_V_a_l_u_e:

     For 'xcmsRaw' objects, if 'rtrange' is NULL, an intensity matrix
     with a row for each 'mzmin', 'mzmax' pair. Columns correspond to
     individual scans. If 'rtrange' is not NULL, a list of two column
     (retention time/intensity) matricies, one for each 'mzmin',
     'mzmax' pair.

     For 'xcmsSet' objects, an 'xcmsEIC' object.

_M_e_t_h_o_d_s:


     _o_b_j_e_c_t = "_x_c_m_s_R_a_w" 'getEIC(object, mzrange, rtrange = NULL, step =
          0.1)'

     _o_b_j_e_c_t = "_x_c_m_s_S_e_t" 'getEIC(object, mzrange, rtrange = 200,
          groupidx,  sampleidx = sampnames(object), rt = c("corrected",
          "raw"))'


_S_e_e _A_l_s_o:

     'xcmsRaw-class', 'xcmsSet-class', 'xcmsEIC-class'

