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Turn a numeric matrix into a mutational-spectrum catalog

Source: R/catalog_attr.R
as_catalog.Rd

Attaches the standard catalog attributes (type, counts_or_density, ref_genome, region, abundance) to x and returns it. No S3 class is set — mSigSpectra catalogs are plain matrices with attributes; functions key off attr(x, "type") via explicit checks.

Usage

as_catalog(
  x,
  type = NULL,
  ref_genome = NULL,
  region = "unknown",
  abundance = NULL,
  counts_or_density = "counts",
  infer_rownames = FALSE
)

Arguments

x

A numeric matrix, data.frame coercible to numeric, or a named numeric vector (converted to a one-column matrix with the vector names as rownames).

type

Optional catalog type identifier ("SBS96", "DBS78", "ID83", etc.). Inferred from nrow(x) if NULL.

ref_genome

Optional BSgenome object or alias; recorded as an attribute and used for abundance lookup.

region

One of "genome", "exome", "transcript", "unknown". For stranded catalogs (SBS192, DBS144) "genome" is silently promoted to "transcript".

abundance

Optional named numeric vector of k-mer counts. If NULL, inferred from shipped all.abundance keyed on ref_genome and region.

counts_or_density

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

infer_rownames

If TRUE and x has no rownames, the canonical rownames for the catalog type are attached (assuming the row order is already correct). If FALSE, x must already have the canonical rownames.

Value

x as a numeric matrix with attributes set.

Examples

m <- matrix(
  1, nrow = 96, ncol = 1,
  dimnames = list(catalog_row_order()$SBS96, "sample1")
)
cat96 <- as_catalog(m)
attr(cat96, "type")   # "SBS96"
#> [1] "SBS96"
attr(cat96, "region") # "unknown"
#> [1] "unknown"