SATS (version 1.0.6)

CalculateSignatureBurdens: Calculate signature burdens

Description

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

Usage

CalculateSignatureBurdens(L, W, H)

Value

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

Arguments

L

Panel size matrix or data frame with samples in columns, see GenerateLMatrix

W

Catalog signature profiles matrix or data frame with signatures in columns

H

Activity matrix or data frame with samples in columns, see EstimateSigActivity

Author

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

Details

The panel size matrix L is of size P (the mutation context) by N (the sample size). The catalog signature profile matrix has dimension of 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. For the catalog signature profile matrix W, reference SBS TMB signature profiles in data(SimData) can be used.

See Also

EstimateSigActivity

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.