fcor-methods             package:msbase             R Documentation

_M_e_t_h_o_d_s _f_o_r _F_u_n_c_t_i_o_n "_f_c_o_r" _i_n _P_a_c_k_a_g_e '_m_s_b_a_s_e'

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

     Methods for function 'fcor' in package '.GlobalEnv'

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

     obx: see above

     oby: see above

   error: measurement error

     ppm: if 'TRUE' then error in parts per million, in arbitrary units
          otherwise

    full: if 'TRUE' then compute for matching and not matching peaks

  weight: if 'TRUE' weight differences between matching peaks.

    uniq: if 'TRUE' compute optimal aligmnent

  method: type of dissimilarity: c("dotprod","soai")

    norm: how to scale the itensities c("student","zscore","tic","no")

   theta: "numeric" how to weight the non-matching peaks.

   range: experimental

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

     The Dissimilarity.

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

     _o_b_x = "_M_a_s_s_v_e_c_t_o_r", _o_b_y = "_M_a_s_s_v_e_c_t_o_r" :

     _o_b_x = "_M_a_s_s_v_e_c_t_o_r_l_i_s_t", _o_b_y = "_M_a_s_s_v_e_c_t_o_r" :

     _o_b_x = "_M_a_s_s_v_e_c_t_o_r_l_i_s_t", _o_b_y = "_N_U_L_L" :

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

     Witold E. Wolski witek96@users.sourceforge.net <URL:
     http://r4proteomics.sourceforge.net>

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

     data(pldata)
     fcor(pldata[[1]],pldata[[2]],error=400,ppm=TRUE,theta=1,weight=FALSE,scale="no",method="dotprod")
     fcor(pldata[[1]],pldata[[2]],error=400,ppm=TRUE,theta=1,weight=FALSE,scale="student",method="soai")
     #search with one peak-list in a bunch of peak-lists
     fcor(pldata,pldata[[1]],error=400,ppm=TRUE,theta=1,weight=FALSE,scale="student",method="soai")
     #compute distance matrix of peak-lists and cluster
     tmp<-fcor(pldata,NULL,error=400,ppm=TRUE,theta=1,weight=FALSE,scale="student",method="soai")
     plot(hclust(tmp,method="average"))

