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Transform a catalog between counts and density

Source: R/catalog_transform.R
transform_catalog.Rd

Converts between counts (raw mutation counts per category) and density (mutations per megabase of context) representations, and between catalog <-> signature (column-normalized) forms. The transformation is expressed by multiplying each category's count by target_abundance[source.n.mer] / source_abundance[source.n.mer], where source.n.mer is the reference context encoded in the row name (first 3 characters for SBS96/192, 5 for SBS1536, 2 for DBS78/144, 4 for DBS136).

Usage

transform_catalog(
  catalog,
  target_ref_genome = NULL,
  target_region = NULL,
  target_counts_or_density = NULL,
  target_abundance = NULL
)

Arguments

catalog

An mSigSpectra catalog (see as_catalog()) with attributes type, counts_or_density, ref_genome, region, abundance.

target_ref_genome, target_region, target_counts_or_density

Target attributes. If NULL, the catalog's current attribute is used.

target_abundance

Optional target abundance vector. If NULL, inferred from target_ref_genome + target_region.

Value

A new catalog (plain matrix with attributes).