getChangedRegions        package:quantsmooth        R Documentation

_g_e_t_C_h_a_n_g_e_d_R_e_g_i_o_n_s

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

     retrieve regions of interest in a vector of intensities using
     quantile smoothing

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

       getChangedRegions(intensities, positions, normalized.to=1, smooth.lambda=2, interval, threshold, minlength=2)

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

intensities: numeric vector

positions: numeric vector of the same length as intensities. If this
          argument is not given the results contain the indexes of the
          'intensities' vector, else the values in 'positions' are
          used. Both vectors are sorted in the order of 'positions'. 

normalized.to: numeric, reference value. Changes are compared to this
          value

smooth.lambda: smoothing parameter

interval: numeric [0,1], bandwidth around reference. If the smoothed
          line at the higher quantile drops below the 'normalized.to'
          value, a deleted region is recognized, and vice versa.

threshold: numeric, if the median smoothed value drops below
          'normalized.to - threshold', or above 'normalized.to +
          threshold' a changed region is called

minlength: integer, not used currently

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

     This function uses 'quantsmooth' to detect regions in the genome
     that are abnormal. If 'interval' is set then a smoothed line is
     calculated for 'tau = 0.5 - interval/2', and a region is
     determined as upregulated if this line is above the reference.
     Down regulation is determined when the smoothed line for 'tau =
     0.5 + interval/2' is below the reference value. If 'threshold' is
     set then a smoothed line is calculated for 'tau = 0.5' and up- or
     down regulation are determined when this line is outside the range
     '[normalized.t - threshold:normalized.to + threshold]'

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

     A data.frame with 3 colums is returned. Each row contains a region
     with columns 'up', 'start' and 'end'. 'start' and 'end' indicate
     positions in the vector of the first and last position that were
     up- or downregulated

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

     Jan Oosting

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

       data(chr14)
       getChangedRegions(ill.cn[,1],ill.pos,normalized.to=2,interval=0.5)

