tsRim-class           package:TargetSearch           R Documentation

_C_l_a_s_s _f_o_r _r_e_p_r_e_s_e_n_t_i_n_g _r_e_t_e_n_t_i_o_n _i_n_d_e_x _m_a_r_k_e_r_s

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

     This is a class to represent retention index markers.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by the function 'ImportFameSettings' or by
     calls of the form 'new("tsRim", limits = [two column matrix with
     time limits], standard = [a vector with RI standards], mass = [m/z
     marker])'.

_S_l_o_t_s:


     '_l_i_m_i_t_s': '"matrix"', two column matrix with lower and upper
          limits where the standards will be search. One row per
          standard. 

     '_s_t_a_n_d_a_r_d': '"numeric"', the marker RI values. 

     '_m_a_s_s': '"numeric"', the m/z marker. 

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


     '_r_i_m_L_i_m_i_t_s' 'signature(obj = "tsRim")': gets the time limits. 

     '_r_i_m_L_i_m_i_t_s<-' 'signature(obj = "tsRim")': sets the time limits. 

     '_r_i_m_M_a_s_s' 'signature(obj = "tsRim")': gets the m/z marker. 

     '_r_i_m_M_a_s_s<-' 'signature(obj = "tsRim")': sets the m/z marker. 

     '_r_i_m_S_t_a_n_d_a_r_d' 'signature(obj = "tsRim")': gets the standars. 

     '_r_i_m_S_t_a_n_d_a_r_d<-' 'signature(obj = "tsRim")': sets the standars. 

_A_u_t_h_o_r(_s):

     Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

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

     'ImportFameSettings'

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

     showClass("tsRim")

     # create a rimLimit object:
     #  - set the lower (first column) and upper (second column) time limites to
     #    search for standards.
     Lim <- rbind(c(200, 300), c(400,450), c(600,650))
     #  - set the retention indices of the standard
     Std <- c(250000, 420000, 630000)
     #  - set the mass marker
     mass <- 87
     #  - create the object
     rimLimits <- new("tsRim", limits = Lim, standard = Std, mass = mass)

     # sometimes you need to change the limits of a particular standard
     rimLimits(rimLimits)[2,] <- c(410, 450)

     # to change the mass value
     rimMass(rimLimits) <- 85

