getSigSegments            package:KCsmart            R Documentation

_R_e_t_r_i_e_v_e _t_h_e _s_i_g_n_i_f_i_c_a_n_t_l_y _g_a_i_n_e_d _a_n_d _l_o_s_t _r_e_g_i_o_n_s _i_n_c_l_u_d_i_n_g _t_h_e _c_o_r_r_e_s_p_o_n_d_i_n_g, _o_r_i_g_i_n_a_l _p_r_o_b_e_s

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

     Retrieve the significantly gained and lost regions including the
     corresponding, original probes. A significance level must be
     selected by the user.

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

     getSigSegments(spm, sigLevels, chromosomes=NULL)

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

     spm: The sample point matrix to be plotted 

sigLevels: The significance thresholds to be used

chromosomes: Takes a vector of chromosomes to be plotted. Defaults to
          all chromosomes. 

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

     'sigLevels' should contain the significance thresholds in a list
     with the positive (gains) threshold in the 'pos' element and the
     negative (losses) threshold in the 'neg' element. This is the
     format as returned by 'findSigLevelTrad' and 'findSigLevelFdr'.

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

     Returns a sigSegments object containing the chromosome, start
     position, end position, average KC score and the mode of the KC
     score in that region of all segments passing the thresholds as set
     in 'sigLevels'.  Additionally, returns the IDs and indices of the
     probes and the positions in the sample point matrix within the
     significant regions. The results are stored in two separate slots:
     'gains' for gains and 'losses' for losses. Use 'write.table' to
     save the results to file.

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

     Jorma de Ronde

_R_e_f_e_r_e_n_c_e_s:

     ~put references to the literature/web site here ~

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

     'findSigLevelTrad',  'findSigLevelTrad', 'write.table'

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

     data(hsSampleData)
     data(hsMirrorLocs)

     spm1mb <- calcSpm(hsSampleData, hsMirrorLocs)

     siglevel1mb <- findSigLevelTrad(hsSampleData, spm1mb, n=3)

     sigSegments1mb <- getSigSegments(spm1mb, siglevel1mb)
     write.table(sigSegments1mb, file=file.path(tempdir(),'sigSegments1mb.txt'))

