fga.func                package:aCGH                R Documentation

_F_u_n_c_t_i_o_n _t_o _c_o_m_p_u_t_e _f_r_a_c_t_i_o_n _o_f _g_e_n_o_m_e _a_l_t_e_r_e_d _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 lists containing proportions of the genome
     that are gained and lost for each sample.

_U_s_a_g_e:

     fga.func(aCGH.obj, thres = 0.25, factor = 2.5, 
              samplenames = sample.names(aCGH.obj), 
              chrominfo = human.chrom.info.Jul03)

_A_r_g_u_m_e_n_t_s:

aCGH.obj: An object of aCGH class

   thres: either a vector providing unique threshold for each sample or
          a vector of the same length as number of samples providing
          sample-specific threshold. If 'aCGH.obj' has non-null
          'sd.samples', then threshold is automatically replaced by
          tumor-specific sd multiplied by 'factor'. Clone is considered
          to be gained if it is above the threshold and lost if it is
          below negative threshold. Defaults to 0.25

  factor: specifies the number by which experimental variability should
          be multiples. Used only when tumor specific variability in
          'aCGH.obj' is not NULL or when factor is greater than 0.
          Defaults to 2.5.

samplenames: Sample names. Default is sample.names(aCGH.obj)

chrominfo: A chromosomal information associated with the mapping of the
          data. Default is human.chrom.info.Jul03 data frame

_V_a_l_u_e:

   gainP: Vector of proportion of genome gained for each sample

   lossP: Vector of proportion of genome lost for each sample

_A_u_t_h_o_r(_s):

     Jane Fridlyand, Ritu Roydasgupta

_E_x_a_m_p_l_e_s:

     data(colorectal)

     col.fga <- fga.func(colorectal, factor=3,chrominfo=human.chrom.info.Jul03)
     cbind(gainP=col.fga$gainP,lossP=col.fga$lossP)[1:5,]

