fractionAltered           package:snapCGH           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:

     fractionAltered(input, thres = 0.25, factor = 2.5, 
              samplenames = colnames(input$M), 
              chrominfo = chrominfo.Mb)

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

   input: An object of type 'MAList' or 'SegList'

   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. 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
          'input' is not NULL or when factor is greater than 0.
          Defaults to 2.5.

samplenames: Sample names. Default is the column names of the
          'aCGHList' object

chrominfo: A chromosomal information associated with the mapping of the
          data. Default is 'chrominfo.Mb'

_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

