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'))

