retcor.peakgroups-methods        package:xcms        R Documentation

_A_l_i_g_n _r_e_t_e_n_t_i_o_n _t_i_m_e_s _a_c_r_o_s_s _s_a_m_p_l_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     These two methods use ``well behaved'' peak groups to calculate
     retention time deviations for every time point of each sample. Use
     smoothed deviations to align retention times.

_A_r_g_u_m_e_n_t_s:

  object: the 'xcmsSet' object

 missing: number of missing samples to allow in retention time
          correction groups 

   extra: number of extra peaks to allow in retention time correction
          correction groups 

  method: either '"loess"' for non-linear alignment or '"linear"' for
          linear alignment 

    span: degree of smoothing for local polynomial regression fitting 

  family: if 'gaussian' fitting is by least-squares with no outlier
          removal, and if 'symmetric' a re-descending M estimator is
          used with Tukey's biweight function, allowing outlier removal 

plottype: if 'deviation' plot retention time deviation points and
          regression fit, and if 'mdevden' also plot peak overall peak
          density and retention time correction peak density 

     col: vector of colors for plotting each sample

      ty: vector of line and point types for plotting each sample

_V_a_l_u_e:

     An 'xcmsSet' object

_M_e_t_h_o_d_s:


     _o_b_j_e_c_t = "_x_c_m_s_S_e_t" 'retcor(object, missing = 1, extra = 1, method
          = c("loess", "linear"), span = .2, family = c("gaussian",
          "symmetric"), plottype = c("none", "deviation", "mdevden"),
          col = NULL, ty = NULL)'


_S_e_e _A_l_s_o:

     'xcmsSet-class', 'loess' 'retcor.obiwarp'

