ValidateSATSInputs: Validate SATS input matrices

In SATS: Signature Analyzer for Targeted Sequencing (SATS)

Validate SATS input matrices

Description

Validate and align SATS mutation-count, panel-context, signature-profile and signature-activity matrices before running refitting or burden calculation.

Usage

ValidateSATSInputs(V=NULL, L=NULL, W=NULL, H=NULL)

Arguments

V	Optional mutation-count matrix or data frame with mutation contexts in rows and samples in columns. Values must be non-negative, finite and integer-like.
L	Optional panel-context matrix or data frame with mutation contexts in rows and samples in columns. Values must be non-negative and finite.
W	Optional catalog signature-profile matrix or data frame with mutation contexts in rows and signatures in columns. Values must be non-negative and finite.
H	Optional signature-activity matrix or data frame with signatures in rows and samples in columns. Values must be non-negative and finite.

Details

ValidateSATSInputs() performs the same matrix-level checks used internally by EstimateSigActivity and CalculateSignatureBurdens. It checks object type, matrix dimensions, numeric values, finite values, non-negative values, duplicated or missing row and column identifiers, mutation-context alignment, sample-ID alignment and signature-name alignment.

When compatible names are present in a different order, the returned matrices are reordered to a common order. For example, L and W are reordered to match V for activity estimation, and L and W are reordered to match H for burden calculation. If one object has names on an axis used for alignment and the paired object does not, or if the named entries differ, the function stops with an informative error. If paired axes are both unnamed, validation proceeds by dimension.

Value

A named list containing the supplied matrices after compatible named axes have been aligned. Objects that were not supplied are omitted from the returned list.

Author(s)

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

See Also

EstimateSigActivity, CalculateSignatureBurdens

Examples

  data(SimData, package="SATS")

  obj <- ValidateSATSInputs(
      V = SimData$V[, 1:3],
      L = SimData$L[, c(3, 1, 2)],
      W = SimData$TrueW_TMB
  )
  identical(colnames(obj$L), colnames(obj$V))

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