EstimateSigActivity: EstimateSigActivity

In SATS: Signature Analyzer for Targeted Sequencing (SATS)

EstimateSigActivity

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)

Arguments

V	Mutation type matrix or data frame with samples in columns
L	Panel size matrix or data frame with samples in columns
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.

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 is used 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.

Value

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

Author(s)

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

See Also

CalculateSignatureBurdens

Examples

    data(SimData, package="SATS")

  
    EstimateSigActivity(SimData$V, SimData$L, SimData$TrueW_TMB)
   

SATS documentation built on Aug. 8, 2025, 6:22 p.m.