03-genSimChroms: Simulating Chromosomes
In MarkRZucker/TACG: Simulating CNV Data

Description Usage Arguments Details Value Author(s) Examples

Simulating chromosomes with clonal or subclonal copy number variations.

1	genSimChroms(N, chr, loci, minLen, maxLen, datapath, chlens, save)

`N`	an integer; the number of simulated chromosomes to be generated.
`chr`	an integer; the total number of germline variants and somatic mutations to simulate in the tumor genome.
`loci`	an integer; the number of single nucleotide polymorphisms (SNPs) to simulate as meaurements made to estimate copy number.
`minLen`	an integer; the minimum length of simulated CNVs.
`maxLen`	an integer; the maximum length of simulated CNVs.
`chlens`	a vector of integers; the lengths of human chrsomosomes.
`save`	a logical value; indicates whether output should be saved.

Each simulated chromosome has a defined number of SNPs, or markers, as determined by the chromosome number and the chromosome lengths used. The positions of each CNV are generated using the minimum and maximum length inputs and the fraction of cells with each CNV are generated by sampling from a dirichlet distribution. Other characteristics - such as whether there are one or two CNVs, and, if two, whether one is nested within the other, are determined by sampling values at random.

The genSimChroms function returns a list of objects, each containing two objects itself: a simulated chromosome (sim) and the data generated therefrom (dat). If the option 'save' is set to TRUE, the function will return no output and instead save the data for each simulation individually in the specified datapath and also save the list of simulated chromosomes (the underlying truth from which the data was generated) as a file 'chrSims.rda' in the specified path.

The sim component contains two objects:

psi: the vector indicating the fraction of cells with each CNV;
clones: a list data frames describing each tumor clone's chromosome segments;

The clones component contains a list of objects, each containing a data frame:

chr: the chromosome number;
start: the start point of each segment;
end: the end point of each segment;
A: an integer; the number of copies of the B allele at each segment;
B: an integer; the number of copies of the A allele at each segment;
parent.index: an integer indicating which clone each clone is descended from;
seg: integer; segment ID;

The dat component is output from the function snpDataGen

Kevin R. Coombes krc@silicovore.com, Mark Zucker zucker.64@buckeyemail.osu.edu

f.loci <- system.file("auxiliary/loci.Rda", package="TACG")
loci <- get(load(f.loci))
f.chlens <- system.file('auxiliary/chlens.Rda',package="TACG")
chlens <- get(load(f.chlens))
temp <- genSimChroms(N=3, chr=17, loci=loci, minLen=200000, maxLen=10000000, datapath=NULL, chlens=chlens, save=FALSE)