calibrate-methods            package:xcms            R Documentation

_C_a_l_i_b_r_a_t_e _p_e_a_k_s _f_o_r _c_o_r_r_e_c_t_i_n_g _u_n_p_r_e_c_i_s_e _m/_z _v_a_l_u_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Calibrate peaks of a xcmsSet via a set of known masses

_A_r_g_u_m_e_n_t_s:

  object: a 'xcmsSet' object with uncalibrated mz

wishlist: a vector or a list of vectors with reference m/z-values

  method: the used calibrating-method, see below

   mzppm: the relative error used for matching peaks in ppm (parts per
          million)

   mzabs: the absolute error used for matching peaks in Da

neighbours: the number of neighbours from wich the one with the highest
          intensity is used (instead of the nearest)

 plotres: can be set to TRUE if wanted a result-plot showing the found
          m/z with the distances and the regression

_V_a_l_u_e:

  object: a 'xcmsSet' with one ore more samples

wishlist: for each sample can be used a different wishlist if there is
          given a list of m/z-vectors. the length of the list must be
          the same as the number of samples, alternatively a single
          vector of masses can be given which is used for all samples.

  method: "shift" for shifting each m/z, "linear" does a linear
          regression and adds a linear term to each m/z. "edgeshift"
          does a linear regression within the range of the mz-wishlist
          and a shift outside.

_M_e_t_h_o_d_s:


     _o_b_j_e_c_t = "_x_c_m_s_S_e_t" ' calibrate(object, wishlist,method="linear",
          mzabs=0.0001, mzppm=5, neighbours=3, plotres=FALSE) '


_S_e_e _A_l_s_o:

     'xcmsSet-class',

