R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Load TITAN parameters

loadDefaultParameters

R Documentation

Load TITAN parameters

Description

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

Usage

  loadDefaultParameters(copyNumber = 5, numberClonalClusters = 1, skew = 0,
      symmetric = TRUE, data = NULL)

Arguments

`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 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.
`symmetric`	`logical`; if `TRUE`, then treat genotypes as symmetric. 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.

Details

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.

Value

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

Author(s)

Gavin Ha <gavinha@gmail.com>

References

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)

Examples

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

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(TitanCNA)
Loading required package: foreach
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/TitanCNA/loadDefaultParameters.Rd_%03d_medium.png", width=480, height=480)
> ### Name: loadDefaultParameters
> ### Title: Load TITAN parameters
> ### Aliases: loadDefaultParameters
> ### Keywords: attribute
> 
> ### ** Examples
> 
>   #### LOAD PARAMETERS ####
>   numClusters <- 2
>   params <- loadDefaultParameters(copyNumber = 5, 
+                                   numberClonalClusters = numClusters)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>