Extract Copy Number Tally Matrix — GetCNTally • utanos

Computes a tally matrix based on copy number (CN) data, either in absolute or relative terms. The function supports the inclusion of additional CN features and allows filtering by specific feature subsets.

Usage

GetCNTally(
  CN_data,
  genome = "hg19",
  relative = FALSE,
  extra_features = FALSE,
  subset_features = NULL
)

Arguments

CN_data: A list of CN features. Typically, this should be the output from functions like ExtractCopyNumberFeatures() or ExtractRelativeCopyNumberFeatures().
genome: A character string specifying the genome build (default: 'hg19'). This parameter is currently unused but can be included for compatibility with future updates.
relative: A logical value. Set to TRUE if using relative copy number data (default: FALSE). If TRUE, the function will use relative feature settings.
extra_features: A logical value indicating whether to include extra CN features in the tally (default: FALSE). When set to TRUE, additional feature settings are applied.
subset_features: A character vector specifying feature names to include in the result. If not NULL, only columns corresponding to these features will be returned.

Value

A matrix where rows represent components (samples) and columns represent CN features. If subset_features is provided, only the specified features are included in the matrix.