01-simplex: Simplices and Clonal Fractions
In CloneFinder: Finding Subclones in SNP and Sequencing Data

Description Usage Arguments Details Value Author(s) Examples

Utility functions for working with vectors of clonal fractions.

1 2	sampleSimplex(n, d = 5) generateSimplex(k, d, reps = 1)

`d`	an integer, the dimension of the simplex, or the number of clones.
`n`	an integer, the number of vectors to sample randomly.
`k`	an integer, the number of equally spaced points to select along each side of the simplex while constructing a lattice.
`reps`	an integer, the number of times to repeat the lattice.

When studying the clonal subpopulations of a tumor sample, we frequently need access to vectors that contain the fraction of cells belonging to each clone. These vectors are characterized by the fact that each entry is nonzero and they must add up to 1. The set of such vectors/points in d-dimensional space defines the "d-simplex". The functions defined here allow us to work with d-simplices, either by randomly sampling vectors (sampleSimplex) or by systematically filling the space with a regular lattice (generateSimplex).

Both functions return a matrix with d columns. Each row contains nonzeo real numbers that sum to 1. The generateSimplex function ensures that (a) each row is unique and (b) the entries in each row appear in decreasing order.

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