This function finds a subset of TMB-based catalog SBS signatures
whose linear combination approximate
de novo SBS signatures detected by signeR.
MappingSignature(W_hat, W_ref=NULL, niter=100, cutoff.I2=0.1, min.repeats=80,
COSMICv="v3.4")A data frame with column names of W_ref (it returns COSMIC SBS names if COSMIC catalog based reference signatures are used) and freq (the number of repetitions greater than cutoff coefficient values out of niter iterations).
Matrix or data frame of de novo signatures from signeR
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).
Number of iterations. The default is 100.
Cutoff value to select signatures. The default is 0.1.
Minimum number of iterations to select signatures with
I^2 > cutoff.I2 . The default is 80.
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".
Donghyuk Lee <dhyuklee@pusan.ac.kr> and Bin Zhu <bin.zhu@nih.gov>
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).