ProfileCleanUp         package:TargetSearch         R Documentation

_R_e_d_u_c_e _r_e_d_u_n_d_a_n_c_y _o_f _t_h_e _p_r_o_f_i_l_e

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

     This function reduces/removes redundancy in a profile.

_U_s_a_g_e:

     ProfileCleanUp(Profile, timeSplit = 500, r_thres = 0.95)

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

 Profile: A 'tsProfile' object. See 'Profile'. 

timeSplit: A RI window. 

 r_thres: A correlation threshold. 

_D_e_t_a_i_l_s:

     Metabolites that are inside a 'timeSplit' window will be
     correlated to see whether the metabolites are the same or not, by
     using 'r_thres' as a cutoff. If so, the intensities and RI will be
     averaged and the metabolite with more correlating masses will be
     suggested.

_V_a_l_u_e:

     A 'tsProfile' object with a non-redundant profile of the masses
     that were searched and correlated, and intensity and RI matrices
     of the correlating masses. 

slot "Info": A data frame with a profile of all masses that correlate
          and the metabolites that correlate in a 'timeSplit' window.

slot "Intensity": A matrix with the averaged intensities of the
          correlating masses.

slot "RI": A matrix with the averaged RI of the correlating masses.

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

     Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

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

     'Profile', 'tsProfile'

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

     # load example data
     require(TargetSearchData)
     data(TargetSearchData)

     # here we use the metabProfile previously calculated and return a "cleaned" profile.
     metabProfile.clean <- ProfileCleanUp(metabProfile, timeSplit = 500,
                           r_thres = 0.95) 

     # Different cutoffs could be specified
     metabProfile.clean <- ProfileCleanUp(metabProfile, timeSplit = 1000,
                           r_thres = 0.9) 

