sim.structure: A function for simulating aCGH data and the corresponding...
In snapCGH: Segmentation, normalisation and processing of aCGH data

Description Usage Arguments Details Value Author(s) References

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 \log_2 ratios. For each simulated clone layout we generate 20 sets of simulated \log_2 ratios from one of five templates. Additionally, we also take account of the cellularity of the test sample in our simulation.

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)

`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`	The upper limit for the length (in Mbs) of a clone (this defaults to 0.2Mb).
`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.

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

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 \log_2 ratios
`datamatrix`	A matrix containing twenty columns each of which contains the simulated \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.