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Read a mutational-spectrum catalog from a file

Source: R/catalog_io.R
read_catalog.Rd

Auto-detects the file format from its first row. Recognized formats:

  • ICAMS native CSV — first N columns are header columns (mutation type, context, etc), remaining columns are per-sample counts / densities.

  • SigProfiler TSV / CSV — single header column with bracketed mutation labels like A[C>A]A, AA[C>A]AA, or PCAWG indel codes like 1:Del:C:0.

  • COSMIC CSV — SBS96 uses the ICAMS-external row-header format; SBS192 uses a stranded variant of the same; DBS78 / ID83 also share their SigProfiler-style layout.

Usage

read_catalog(
  file,
  ref_genome = NULL,
  region = "unknown",
  counts_or_density = "counts",
  format = c("auto", "ICAMS", "SigProfiler", "COSMIC")
)

Arguments

file

Path to the catalog file.

ref_genome

Optional BSgenome object or alias; stored as attribute.

region

One of "genome", "exome", "transcript", "unknown".

counts_or_density

One of "counts", "density", "counts.signature", "density.signature".

format

"auto" (default), "ICAMS", "SigProfiler", or "COSMIC". In "auto" mode the format is inferred from the file's first data row.

Value

A catalog matrix with attributes (see as_catalog()).

Details

The matrix is reordered to the canonical rownames for its type and wrapped in a catalog via as_catalog().