optimize_exposure_QP {mSigTools}

Quadratic programming optimization of signature activities

Description

Quadratic programming optimization of signature activities

Usage

optimize_exposure_QP(spectrum, signatures)

Arguments

spectrum

Mutational signature or mutational spectrum as a numeric vector or single column data frame or matrix.

signatures

Matrix or data frame of signatures from which to reconstruct spectrum. Rows are mutation types and columns are signatures. Should have column names for interpretable results. Cannot be a vector because the column names are needed.

Details

Code adapted from SignatureEstimation::decomposeQP and uses solve.QP in package quadprog.

Value

A vector of exposures with names being the colnames from signatures.

Examples

usigs <- matrix(c(0.2, 0.7, 0.1,
                  0.3, 0.6, 0.1,
                  0.1, 0.1, 0.8), nrow = 3)
colnames(usigs) <- c("u1", "u2", "u3")
tsig <- matrix(c(0.25, 0.65, 0.1), nrow = 3)
optimize_exposure_QP(tsig, usigs)