02-WeightVector: Class "WeightVector"

In CloneFinder: Finding Subclones in SNP and Sequencing Data

Description

A class, with validity checking, to contain vectors of non-negative real numbers whose sum equals one.

Usage

WeightVector(phi)

Arguments

phi	a numeric vector containing non-negative values.

Details

When trying to simulate or model biological data from (sub)clonal populations of cells, we need vectors that keep track of the fraction of cells belonging to each clone. These vectors can only contain non-negative entries, and the entries must add up to one. (We thought about calling these things "ClonalFractions", but that seems overly specialized for a notion that is likely to prove useful in other contexts.) Such vectors of length d can also be viewed as points of a d-dimensional simplex.

We have implemented WeightVectors as an S4 class, primarily so we can enforce the defining properties. We also expect this design to make it easier to use them as slots in other classes.

Value

The constructor returns a valid object of the WeightVector class.

Objects from the Class

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

Slots

psi

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

Methods

coerce(from, to, strict = TRUE)

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

Author(s)

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

See Also

Simplices

Examples

showClass("WeightVector")

WeightVector(1:4)
as(WeightVector(c(2, 3, 5)), "numeric")

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