MappingSignature: Find a subset of TMB-based catalog SBS signatures
In SATS: Signature Analyzer for Targeted Sequencing (SATS)

MappingSignature

R Documentation

Find a subset of TMB-based catalog SBS signatures

Description

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

Usage

 MappingSignature(W_hat, W_ref=NULL, niter=100, cutoff.I2=0.1, min.repeats=80, 
                         COSMICv="v3.4")

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 `RefTMB$TMB_SBS_v3.2` or `RefTMB$TMB_SBS_v3.4` depending on the value of `COSMICv` below (see `RefTMB`).
`niter`	Number of iterations. The default is 100.
`cutoff.I2`	Coefficient cutoff used to select reference signatures. The default is 0.1, requiring a retained reference signature to contribute more than 10 percent to a `de novo` profile in a repeated fit.
`min.repeats`	Minimum number of repeated fits in which a reference signature must satisfy `coeff > cutoff.I2`. The default is 80.
`COSMICv`	Version of the TMB-based COSMIC signatures ("v3.2" or "v3.4"). This option is ignored if `W_ref` is not `NULL`. The default is "v3.4".

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 cutoff.I2 in at least min.repeats repeats. With the default settings, a retained signature must have a coefficient greater than 0.1 in at least 80 of 100 repeated fits.

Value

A data frame with one row per retained reference signature. The Reference column contains the corresponding column names of W_ref (COSMIC SBS names when the default COSMIC reference matrix is used), and freq gives the number of repeated fits in which the signature coefficient exceeded cutoff.I2.