03-Tumor: Class "Tumor"

In CloneFinder: Finding Subclones in SNP and Sequencing Data

Description

A class that represents tumors, thought of as a collection of (sub)clones each with an associated measure as a fraction of all tumor cells.

Usage

Tumor(psi, rounds, nu = 100, pcnv = 0.5, norm.contam = FALSE, cnmax = 4)
getClone(tumor, i)

Arguments

psi	a numeric vector containing non-negative values.
rounds	an integer; the number of generations through which to evolve the potential clones.
nu	an integer; the expected number of mutations in each clonal generation.
pcnv	a real number between 0 and 1; the probability of a CNV occuring per generation.
norm.contam	a logical value; should we treat one of the cell populations as normal cells that are "contaminating" the tumor specimen?
cnmax	an integer, the maximum copy number allowed in the simulated data.
tumor	an object of the Tumor class.
i	a integer; which clone to extract.

Details

The Tumor class is used to represent compex tumors, each of which consists a set of subclones representing different fractional parts of the tumor. Each clone is characterized by a set of copy number variants (modeled by the output produced by something like the DNAcopy package) and, optionally, a set of sequence mutations. Each of these genetic events is mapped to a specific interval or point in the human genome.

In the current implementation, a Tumor consists of a weight vector that specifies the fractions of cells for each clone and a list of clones. At present, each clone is itself a list containing one (if there are no mutations) or two (if there are both copy number variants and mutations) data frames. This structure is likely to change in later versions of the package, since we expect to implement a full-fledged S4 class to represent clones. So, one should not rely on the current implementation.

Value

The constructor returns a valid object of the Tumor class.

Objects from the Class

Although objects can be created using new, the preferred method is to use the constructor function, Tumor.

Slots

psi

a WeightVector containing non-negative values whose sum equals one.

clones

a list, each of whose elements represents a clone.

Methods

coerce(from, to, strict = TRUE)

Convert the Tumor object into a simple numeric vector. Never actually used in this form, since the preferred method is to write as(WV, "list").

Author(s)

Kevin R. Coombes [e-mail], Mark Zucker [e-mail]

See Also

WeightVector

Examples

showClass("Tumor")

tumor <- Tumor(c(0.5, 0.3, 0.2), 100)
simpleTumor <- as(tumor, "list")
reformed <- as(simpleTumor, "Tumor")

CloneFinder documentation built on May 2, 2019, 5:01 p.m.