optimize_exposure_QP

Quadratic programming optimization of signature activities

Utility functions for mutational signature analysis
as described in Alexandrov, L. B. (2020)
<doi:10.1038/s41586-020-1943-3>.
This package provides two groups of functions. One is
for dealing with mutational signature "exposures"
(i.e. the counts of mutations in a sample that are
due to each mutational signature). The other group of
functions is for matching or comparing sets of
mutational signatures. 'mSigTools' stands for
mutational Signature analysis Tools.

Steven Rozen

mSigTools

Mutational Signature Analysis Tools

Nanhai Jiang

optimize_exposure_QP function

<dl><dt>spectrum</dt>
<dd>Mutational signature or mutational spectrum
as a numeric vector or single column data frame or matrix.</dd>
<dt>signatures</dt>
<dd>Matrix or data frame of signatures from which to
reconstruct <code>spectrum</code>. 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.</dd></dl>

Arguments

Quadratic programming optimization of signature activities — optimize_exposure_QP

<dl>

<dt>spectrum</dt>
<dd>Mutational signature or mutational spectrum
as a numeric vector or single column data frame or matrix.</dd>


<dt>signatures</dt>
<dd>Matrix or data frame of signatures from which to
reconstruct <code>spectrum</code>. 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.</dd>

</dl>

optimize_exposure_QP: Quadratic programming optimization of signature activities

Description

Usage

Value

Arguments

Details

Examples