SATS (version 1.0.6)

EstimateSigActivity: Estimate signature activity

Description

Estimation of signature activities given the original mutation type matrix, the panel size matrix, and the catalog signature profile matrix.

Usage

EstimateSigActivity(V, L, W, n.start=50, iter.max=5000, eps=1e-5)

Value

A list containing the estimated activity matrix H, the log-likelihood loglike, and the logical value converged.

Arguments

V

Mutation type matrix or data frame with samples in columns

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

n.start

Number of initializations. The default is 50.

iter.max

Maximum number iterations in the EM algorithm. The default is 5000.

eps

Stopping tolerance in the EM algorithm. The default is 1e-5.

Author

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

Details

The panel size matrix L and mutation type matrix V are 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). For single base substitutions (SBS), P is 96. For the objects V, L, and W, we must have dim(V) = dim(L) and ncol(W) = K, where K is the number of signatures. EstimateSigActivity() uses the EM algorithm to estimate signature n.start, iter.max and eps control EM part. Because the convergence to a local saddle point can be an issue of the EM algorithm, it would be good practice to try multiple initial values (n.start, the default is 50). For each initial value, the default value of the maximal iteration of the EM algorithm (iter.max) is 5000, and the stopping tolerance (eps) is set to 1e-5. For the catalog signature profile matrix W, reference SBS TMB signature profiles in data(SimData) can be used.

See Also

CalculateSignatureBurdens

Examples

    data(SimData, package="SATS")
  # \donttest{
    EstimateSigActivity(SimData$V, SimData$L, SimData$TrueW_TMB)
  # } 
  # For more detailed usage, please refer to README and the user manual
  # in https://github.com/binzhulab/SATS/tree/main.