CalculateSigExpectancy: CalculateSignatureBurdens
In SATS: Signature Analyzer for Targeted Sequencing (SATS)
CalculateSignatureBurdens R Documentation
CalculateSignatureBurdens
Description
Estimation of the expected number of mutations attributed
by TMB-based catalog signatures (signature expectancy) given
the panel size matrix, the catalog signature profile matrix
and the signature activities matrix.
Usage
CalculateSignatureBurdens(L, W, H)
Arguments
L
Panel size matrix or data frame with samples in columns
W
Catalog signature profiles matrix or data frame with signatures in columns
H
Activity matrix or data frame with samples in columns
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.
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 <dhyuklee@pusan.ac.kr> and Bin Zhu <bin.zhu@nih.gov>
See Also
EstimateSigActivity
Examples
data(SimData, package="SATS")
CalculateSignatureBurdens(SimData$L, SimData$TrueW_TMB, SimData$TrueH)
SATS documentation built on Aug. 8, 2025, 6:22 p.m.
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| CalculateSignatureBurdens | R Documentation |
CalculateSignatureBurdens
Description
Estimation of the expected number of mutations attributed by TMB-based catalog signatures (signature expectancy) given the panel size matrix, the catalog signature profile matrix and the signature activities matrix.
Usage
CalculateSignatureBurdens(L, W, H)
Arguments
L |
Panel size matrix or data frame with samples in columns |
W |
Catalog signature profiles matrix or data frame with signatures in columns |
H |
Activity matrix or data frame with samples in columns |
Details
The panel size matrix L is of size P (the mutation context) by N
(the sample size). The catalog signature profile matrix has dimension
of P by K (the number of signatures) and the activity matrix H is of
size K by N. For single base substitutions (SBS), P is 96.
If K is the number of signatures and N is
the number of samples, then H must be of dimension K X N,
ncol(L) = N, and ncol(W) = K.
Value
A matrix of dimension K X N, where K is the number
of signatures and N is the number of samples.
Author(s)
Donghyuk Lee <dhyuklee@pusan.ac.kr> and Bin Zhu <bin.zhu@nih.gov>
See Also
EstimateSigActivity
Examples
data(SimData, package="SATS")
CalculateSignatureBurdens(SimData$L, SimData$TrueW_TMB, SimData$TrueH)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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