simulateData             package:snapCGH             R Documentation

_A _f_u_n_c_t_i_o_n _f_o_r _s_i_m_u_l_a_t_i_n_g _a_C_G_H _d_a_t_a _a_n_d _t_h_e _c_o_r_r_e_s_p_o_n_d_i_n_g _c_l_o_n_e _l_a_y_o_u_t

_D_e_s_c_r_i_p_t_i_o_n:

     This simulation scheme operates in two stages. Initially, we
     simulate the layout of clones before using a modified version of
     the scheme developed by Willenbrock et al., 2005 to generate the
     $\mbox{log}_2$ ratios. For each simulated clone layout we generate
     20 sets of simulated $\mbox{log}_2$ ratios from one of five
     templates. Additionally, we also take account of the cellularity
     of the test sample in our simulation.

_U_s_a_g_e:

     simulateData(nArrays = 20, chrominfo = NULL, prb.short.tiled = 0.5,
                      prb.long.tiled = 0.5, non.tiled.lower.res = 0.9,
                      non.tiled.upper.res = 1.1, length.clone.lower = 0.05,
                      length.clone.upper = 0.2, tiled.lower.res = -0.05,
                      tiled.upper.res = 0, sd = NULL, output = FALSE,
                      prb.proportion.tiled = c(0.2, 0.2, 0.2, 0.2, 0.2),
                      zerolengthnontiled = NULL, zerolengthtiled = NULL,
                      nonzerolengthnontiled = NULL, nonzerolengthtiled =
                      NULL, seed = 1)

_A_r_g_u_m_e_n_t_s:

 nArrays: The number of arrays we want to simulate 

chrominfo: The information about chromosome length/centromere location
          to be used. Defaults to the information provided in aCGH
          package of Jane Fridlyand and Peter Dimitrov. 

prb.short.tiled: The probability of a tiled region on the short arm of
          the simulated chromosome (defaults to 0.5).

prb.long.tiled: The probability of a tiled region on the long arm of
          the simulated chromosome (defaults to 0.5).

non.tiled.lower.res: The lower limit for the distance (in Mbs) between
          adjacent clones in non-tiled regions of the genome (defaults
          to 0.9Mb).

non.tiled.upper.res: The upper limit for the distance (in Mbs) between
          adjacent clones in non-tiled regions of the genome (defaults
          to 1.1Mb). 

length.clone.lower: The lower limit for the length (in Mbs) of a clone
          (this defaults to 0.05Mb). 

length.clone.upper: 

tiled.lower.res: The lower limit for the distance (in Mbs) between
          adjacent clones in tiled regions of the genome (defaults to
          -0.05Mb). 

tiled.upper.res: The upper limit for the distance (in Mbs) between
          adjacent clones in tiled regions of the genome (defaults to
          0Mb). 

      sd: The standard deviation of the simulated data in each of the
          states. Defaults to being randomly sampled between 0.1 and
          0.2. 

  output: A logical variable which is TRUE if you want the output to be
          written to txt files in the present working directory.
          Defaults to FALSE. 

prb.proportion.tiled: Given that an arm of a chromosome contains a
          tiled region this variable (which is a vector of length 5)
          gives the probability that 20,30,40,50 or 100% of the
          chromosome is tiled. It defaults to (0.2,0.2,0.2,0.2,0.2) 

zerolengthnontiled: The empirical distribution for regions of the
          genome which are non-tiled and contain no copy number gains
          or losses. Defaults to zero.length.distr.non.tiled 

zerolengthtiled: The empirical distribution for regions of the genome
          which are tiled and contain no copy number gains or losses.
          Defaults to zero.length.distr.tiled 

nonzerolengthnontiled: The empirical distribution for regions of the
          genome which are non-tiled and contain no copy number gains
          or losses. Defaults to non.zero.length.distr.non.tiled 

nonzerolengthtiled: The empiricial distribution for regions of the
          genome which are tiled and contain copy number gains or
          losses. Defaults to non.zero.length.distr.tiled 

    seed: Seed value allowing simulation to be reproduced if the same
          seed value is set.

_D_e_t_a_i_l_s:

     For more details see the article by Marioni and Thorne published
     in Bioinformatics.

_V_a_l_u_e:

     The function returns a list containing the following elements. 

  clones: Gives the start, end and midpoint of the simulated clones.

class.output : A list of the true underlying state clones are assigned
          to for each of the twenty simulations associated with each
          clone layout.

class.matrix: Defines the true underlying state clones are assigned to
          in each of the five classes

 classes: Which of the five class outputs has been used to simulate the
          $\mbox{log}_2$ ratios

datamatrix: A matrix containing twenty columns each of which contains
          the simulated $\mbox{log}_2$ ratios associated with each of
          the simulations for a particular clone layout.

 samples: Gives information about the cellularity associated with each
          of the samples.

_A_u_t_h_o_r(_s):

     John Marioni and Natalie Thorne

_R_e_f_e_r_e_n_c_e_s:

     See the relevant article in Bioinformatics or the following
     website: www.damtp.cam.ac.uk/user/jcm68

_E_x_a_m_p_l_e_s:

