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.
1 2 3  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 

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 
alleleEmissionModel 
Specify the emission model to use for the allelic input data. 
symmetric 

data 

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 nonreference alleles the same. For example, genotypes AA
(homozygous for reference allele) and BB
(homozygous for nonreference 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: 18811893. (PMID: 25060187)
1 2 3 4  #### LOAD PARAMETERS ####
numClusters < 2
params < loadDefaultParameters(copyNumber = 5,
numberClonalClusters = numClusters)

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