CalculateSignatureBurdens: Calculate signature burdens

In SATS: Signature Analyzer for Targeted Sequencing (SATS)

Calculate signature burdens

Description

Estimation of the expected number of mutations attributed by TMB-based catalog signatures (signature burden) given the sample-level panel-context matrix, the catalog signature-profile matrix and the signature activities matrix.

Usage

 CalculateSignatureBurdens(L, W, H)

Arguments

L	Sample-level panel-context matrix or data frame with samples in columns, see GenerateLMatrix
W	Catalog signature-profile matrix or data frame with signatures in columns
H	Activity matrix or data frame with samples in columns, see EstimateSigActivity

Details

The sample-level panel-context matrix L is of size P (the mutation context) by N (the sample size). The catalog signature-profile matrix W has dimension P by K (the number of signatures) and the activity matrix H is of size K by N. For single base substitutions (SBS), P is 96. If K is the number of signatures and N is the number of samples, then H must be of dimension K X N, ncol(L) = N, and ncol(W) = K. The input matrices must contain numeric, finite and non-negative values. When row names and column names are present, CalculateSignatureBurdens() checks that L, W and H contain matched mutation contexts, signature names and sample IDs. If the same names are present in a different order, L and W are reordered to match H. If one object has names on an axis used for alignment and the paired object does not, or if the named entries differ between matrices, the function stops with an informative error. Users can run ValidateSATSInputs directly to check and align inputs before calling this function. For the catalog signature profile matrix W, reference SBS TMB signature profiles in data(SimData) can be used.

Value

A matrix of dimension K X N, where K is the number of signatures and N is the number of samples.

Author(s)

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

See Also

EstimateSigActivity, ValidateSATSInputs

Examples

    data(SimData, package="SATS")

    CalculateSignatureBurdens(SimData$L, SimData$TrueW_TMB, SimData$TrueH)
    # For more detailed usage, please refer to README and the user manual
    # in https://github.com/binzhulab/SATS/tree/main.

SATS documentation built on Sept. 16, 2026, 1:06 a.m.