loadDefaultParameters: Load TITAN parameters
In ATLi2001/titancna: Subclonal copy number and LOH prediction from whole genome sequencing of tumours

Description Usage Arguments Details Value Author(s) References See Also Examples

Load TITAN model parameters based on maximum copy number and number of clonal clusters.

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  loadDefaultParameters(copyNumber = 5, numberClonalClusters = 1, skew = 0,
      hetBaselineSkew = NULL, alleleEmissionModel = "binomial", 
      symmetric = TRUE, data = NULL)

`copyNumber`	Maximum number of absolute copies to account for in the model. Default (and recommended) is 5.
`numberClonalClusters`	Number of clonal clusters to use in the analysis. Each cluster represents a potential clone. Using ‘1’ treats the sample as being clonal (no subclonality). ‘2’ or higher treats the tumour data as being subclonal.
`skew`	`numeric` float (between 0 to 0.5) indicating the heterozygous baseline shift for the allelic ratios towards 1. This is may be required for SOLiD data, but for most cases, this argument can be omitted. Use `0` or `NULL` for no skew.
`hetBaselineSkew`	Allelic reference base skew for heterozygous states (e.g. 1:1, 2:2, 3:3). Value is additive to baseline allelic ratios (which may already be adjusted by `skew`). Use `0` or `NULL` for no skew; use from range between 0 to 0.5.
`alleleEmissionModel`	Specify the emission model to use for the allelic input data. `"binomial"` or `"Gaussian"`.
`symmetric`	`logical`; if `TRUE`, then treat genotypes as symmetric. This should always be `TRUE` because `symmetric=FALSE` is deprecated. See Details.
`data`	`data` is the output of function `loadAlleleCounts`. If provided and `symmetric=TRUE`, then it will compute the median allelic ratio to use as the baseline for heterozygous genotypes; otherwise, the baseline will default to 0.55 (reference/depth) if `data=NULL`. If `symmetric=FALSE`, this argument will not be used.

Generally, TitanCNA should be run once for each number of clonal clusters in the range of 1 to 5. Then, use model selection to choose the run with the optimal number of clusters.

If the allelic ratio data is skewed towards one allele, then use skew to help define the baseline. For example, if the data is skewed towards the reference, then use 0.1 so that the heterozygous baseline is at 0.6. The allelic ratio baseline is normally at 0.5.

sParams, which represents the parameters for estimation of subclonality, always contains values for one cluster that represents the clonally dominant cluster (events present in nearly all tumour cells) with an initial value of sParams$s_0[1] = 0.001.

Setting symmetric to TRUE will treat reference and non-reference alleles the same. For example, genotypes AA (homozygous for reference allele) and BB (homozygous for non-reference allele) as being equivalent. This will reduce the state space substantially.

list containing 4 sets of parameters, each as a component:

`genotypeParams`	Parameters for copy number and allelic ratios geneotype states
`normalParams`	Parameters for normal contamination
`ploidyParams`	Parameters for average tumour ploidy
`sParams`	Parameters for modeling subclonality: clonal clusters and cellular prevalence

Gavin Ha <gavinha@gmail.com>

Ha, G., Roth, A., Khattra, J., Ho, J., Yap, D., Prentice, L. M., Melnyk, N., McPherson, A., Bashashati, A., Laks, E., Biele, J., Ding, J., Le, A., Rosner, J., Shumansky, K., Marra, M. A., Huntsman, D. G., McAlpine, J. N., Aparicio, S. A. J. R., and Shah, S. P. (2014). TITAN: Inference of copy number architectures in clonal cell populations from tumour whole genome sequence data. Genome Research, 24: 1881-1893. (PMID: 25060187)

loadAlleleCounts

  #### LOAD PARAMETERS ####
  numClusters <- 2
  params <- loadDefaultParameters(copyNumber = 5, 
                                  numberClonalClusters = numClusters)