retcor-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 _w_i_t_h _O_b_i_w_a_r_p

_D_e_s_c_r_i_p_t_i_o_n:

     Calculate retention time deviations for each sample. It is based
     on the code at <URL: http://obi-warp.sourceforge.net/>. However,
     this function is able to align multiple samples, by a center-star
     strategy. 

     For the original publication see

     Chromatographic Alignment of ESI-LC-MS Proteomics Data Sets by
     Ordered Bijective Interpolated Warping John T. Prince and, Edward
     M. Marcotte Analytical Chemistry 2006 78 (17), 6140-6152

_A_r_g_u_m_e_n_t_s:

  object: the 'xcmsSet' object

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

profStep: step size (in m/z) to use for profile generation from the raw
          data files

       r: Responsiveness of warping.  0 will give a linear warp based
          on start and end points.  100 will use all bijective anchors

       g: Gap penalty given in comma separated string: initiate,extend
          (*)Defaults: (gap_init,gap_extend) [by score type]: 'cor' =
          '0.3,2.4' 'cov' = '0,11.7' 'prd' = '0,7.8' 'euc' = '0.9,1.8'

     cor: Score function: (*)cor (Pearson's R) or cor_opt (better
          runtime), cov (covariance), prd (product), euc (Euclidean
          distance)

       l: Local rather than *global alignment

     i\_: Penalty for initiating alignment (for local alignment only)
          (*)Default: 0

_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, method="obiwarp", plottype =
          c("none", "deviation", "mdevden"),col = NULL, ty = NULL,
          profStep=1, r=NULL, g=NULL, cor = NULL, l=NULL, i_=0) 

_S_e_e _A_l_s_o:

     'xcmsSet-class',

