idPoints               package:KCsmart               R Documentation

_I_d_e_n_t_i_f_y _p_o_i_n_t_s _i_n _s_a_m_p_l_e _p_o_i_n_t _m_a_t_r_i_x _p_l_o_t

_D_e_s_c_r_i_p_t_i_o_n:

     Identify points in sample point matrix plot

_U_s_a_g_e:

     idPoints(spm, mode='pos', dev=2, chromosomes=NULL)

_A_r_g_u_m_e_n_t_s:

     spm: The sample point matrix object of which points are to be
          identified 

    mode: Determines which points will be identified: mode='pos' will
          identify points in gained regions, mode='neg' will identify
          points in lost regions 

     dev: The device on which the sample point matrix was plotted

chromosomes: 

     { If not all chromosomes contained in the sample point matrix were
     plotted (using the 'chromosomes' argument in the 'plot' command),
     the same chromosomes must be entered here as an argument}

_D_e_t_a_i_l_s:

     Using the mouse pointer points in a sample point matrix plot can
     be identified by left-clicking on the to-be-identified points.
     Right-clicking exits the selection and returns the selected
     points.

_V_a_l_u_e:

     Returns a data.frame listing the the position and the KC score for
     each identified point. 

 KCscore: KCscore of the identified point

chromosome: Chromosome on which the identified point is located

chromPosition: Position on the chromosome of the identified point

   colin: Co-linear location of the identified point (given the
          selected chromosomes)

_A_u_t_h_o_r(_s):

     Jorma de Ronde

_S_e_e _A_l_s_o:

     'plot'

_E_x_a_m_p_l_e_s:

     data(hsSampleData)
     data(hsMirrorLocs)

     #spm1mb <- calcSpm(hsSampleData, hsMirrorLocs)

     #plot(spm1mb, type=1)
     #idPoints(spm1mb)

     #x11()
     #plot(spm1mb, chromosomes=c(1,2,5))
     #idPoints(spm1mb, mode='neg', dev=3, chromosomes=c(1,2,5))

