getintcalib-methods         package:mscalib         R Documentation

_O_b_t_a_i_n _c_a_l_i_b_r_a_t_i_o_n _c_o_e_f_f_i_c_i_e_n_t_s _u_s_i_n_g _i_n_t_e_r_n_a_l _c_a_l_i_b_r_a_t_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     Obtain calibration coefficients using internal calibration.

_A_r_g_u_m_e_n_t_s:

  object: 'Massvector-class' or 'Massvectorlist-class'

   calib: 'Massvector-class' with calibratio masses _e.g._ 'cal2',
          'cal'

   error: Size of the search window used to find matching masses.

    uniq: If crossing matches should be resolved

     ppm: Is the 'error' specified in parts per million or in arbitrary
          units _e.g_ Dalton

  weight: should weighted linear regression be used?  default is
          'FALSE' - no

interfix: default 'FALSE'. If 'TRUE' fix the  slope if 'ppm=FALSE', fix
          intercept otherwise.

_M_e_t_h_o_d_s:


     _o_b_j_e_c_t = "_M_a_s_s_v_e_c_t_o_r", _c_a_l_i_b = "_M_a_s_s_v_e_c_t_o_r" returns
          'Massvector-class'

     _o_b_j_e_c_t = "_M_a_s_s_v_e_c_t_o_r_l_i_s_t", _c_a_l_i_b = "_M_a_s_s_v_e_c_t_o_r" returns
          'Massvectorlist-class'

_S_e_e _A_l_s_o:

     'getintcalib-methods' , 'Calibstat-class' ,'Calibintstat-class'
     ,'Caliblist-class' ,'Calibintlist-class'

_E_x_a_m_p_l_e_s:

     library(msbase)
     data(pldata)
     data(cal2)
     intcalib <- getintcalib(pldata,cal2,error=400,ppm=TRUE)
     image(intcalib,what="Coeff.Intercept")
     tmp <- applycalib(pldata,intcalib)

