MappingSignature: Find a subset of TMB-based catalog SBS signatures

In SATS: Signature Analyzer for Targeted Sequencing (SATS)

Find a subset of TMB-based catalog SBS signatures

Description

This function finds a subset of TMB-based catalog SBS signatures whose linear combination approximate de novo SBS signatures detected by signeR.

Usage

 MappingSignature(W_hat, W_ref=NULL, niter=100, cutoff.I2=0.1, min.repeats=80)

Arguments

W_hat	Matrix or data frame of de novo signatures from signeR
W_ref	NULL or a matrix or data frame of TMB-based catalog signatures. If NULL, then it will default to SimData$W_TMB (see SimData).
niter	Number of iterations. The default is 100.
cutoff.I2	Cutoff value to select signatures. The default is 0.1.
min.repeats	Minimum number of iterations to select signatures with I^2 > cutoff.I2 . The default is 80.

Details

MappingSignature() applies penalized non-negative least squares (pNNLS) for selecting the TMB-based catalog signatures. Specifically, it repeats pNNLS 100 times (niter) to reduce the randomness of cross-validation involved in pNNLS. Then TMB-based catalog signatures are selected with a coefficient greater than 0.1 (cutoff.I2) in more than 80 repeats (min.repeats).

Value

A data frame with column names of W_ref (it returns COSMIC SBS names if COSMIC catlog based reference signatures are used) and freq (the number of repetitions greater than cutoff coefficient values out of niter iterations).

Author(s)

Donghyuk Lee <[e-mail]> and Bin Zhu <[e-mail]>

SATS documentation built on Aug. 8, 2025, 6:22 p.m.