decompose: Decomposes the mutational spectrum of a genome in terms of...

In parklab/SigMA: Signature Multivariate Analysis

Decomposes the mutational spectrum of a genome in terms of tumor type specific signatures that were calculated through analysis of public WGS samples from ICGC and TCGA consortia, and contained as a list in the package. Non-negative-least squares algorithm is used and the number of signatures to be considered in the decomposition is increased gradually, first all pairs from among the available signatures are considered and minimal error pair is kept. Then all 3-signature combinations, 4-signature combinations and so on are considered. The result is updated if the error is smaller with larger number of signatures

Description

Decomposes the mutational spectrum of a genome in terms of tumor type specific signatures that were calculated through analysis of public WGS samples from ICGC and TCGA consortia, and contained as a list in the package. Non-negative-least squares algorithm is used and the number of signatures to be considered in the decomposition is increased gradually, first all pairs from among the available signatures are considered and minimal error pair is kept. Then all 3-signature combinations, 4-signature combinations and so on are considered. The result is updated if the error is smaller with larger number of signatures

Usage

decompose(spect, signatures, data)

Arguments

spect	composite spectrum that is being decomposed
signatures	a data.frame that contains the signatures in its columns
data	sequencing platform that as in run(), used for setting the maximum number of signatures that is allowed in the decomposition

parklab/SigMA documentation built on Aug. 11, 2024, 8:49 p.m.