threshold.func             package:aCGH             R Documentation

_F_u_n_c_t_i_o_n _t_o _i_n_d_i_c_a_t_e _g_a_i_n _o_r _l_o_s_s _f_o_r _e_a_c_h _c_l_o_n_e _f_o_r _e_a_c_h _s_a_m_p_l_e

_D_e_s_c_r_i_p_t_i_o_n:

     This function outputs a matrix containing gain/loss indicator for
     each clone and sample.

_U_s_a_g_e:

     threshold.func(dat, posThres, negThres = NULL)

_A_r_g_u_m_e_n_t_s:

     dat: log2ratios of the relevant array CGH object

posThres: Global or sample-specific threshold for gain

negThres: Global or sample-specific threshold for loss. Defaults to
          -posThres

_V_a_l_u_e:

     Returns a matrix with a row for each clone and column for each
     sample. "1" indicates gain and "-1" indicates loss.

_A_u_t_h_o_r(_s):

     Jane Fridlyand, Ritu Roydasgupta

_E_x_a_m_p_l_e_s:

     data(colorectal)

     factor <- 3
     tbl <- threshold.func(log2.ratios(colorectal),posThres=factor*(sd.samples(colorectal)$madGenome))
     rownames(tbl) <- clone.names(colorectal)
     colnames(tbl) <- sample.names(colorectal)
     tbl[1:5,1:5]

