ICAMS (version 2.1.2)

TransformCatalog: Transform between counts and density spectrum catalogs and counts and density signature catalogs.

Description

Transform between counts and density spectrum catalogs and counts and density signature catalogs.

Usage

TransformCatalog(
  catalog,
  target.ref.genome = NULL,
  target.region = NULL,
  target.catalog.type = NULL,
  target.abundance = NULL
)

Arguments

catalog

An SBS or DBS catalog as described in ICAMS; must not be an ID (small insertion and deletion) catalog.

target.ref.genome

A ref.genome argument as described in ICAMS. If NULL, then defaults to the ref.genome attribute of catalog.

target.region

A region argument; see as.catalog and ICAMS. If NULL, then defaults to the region attribute of catalog.

target.catalog.type

A character string acting as a catalog type identifier, one of "counts", "density", "counts.signature", "density.signature"; see as.catalog. If NULL, then defaults to the catalog.type attribute of catalog.

target.abundance

A vector of counts, one for each source K-mer for mutations (e.g. for strand-agnostic single nucleotide substitutions in trinucleotide -- i.e. 3-mer -- context, one count each for ACA, ACC, ACG, ... TTT). See all.abundance. If NULL, the function tries to infer target.abundace from the class of catalog and the value of the target.ref.genome, target.region, and target.catalog.type. If the target.abundance can be inferred and is different from a supplied non-NULL value of target.abundance, raise an error.

Value

A catalog as defined in ICAMS.

Details

Only the following transformations are legal:

1. counts -> counts (deprecated, generates a warning; we strongly suggest that you work with densities if comparing spectra or signatures generated from data with different underlying abundances.)

2. counts -> density

3. counts -> (counts.signature, density.signature)

4. density -> counts (the semantics are to infer the genome-wide or exome-wide counts based on the densities)

5. density -> density (a null operation, generates a warning)

6. density -> (counts.signature, density.signature)

7. counts.signature -> counts.signature (used to transform between the source abundance and target.abundance)

8. counts.signature -> density.signature

9. counts.signature -> (counts, density) (generates an error)

10. density.signature -> density.signature (a null operation, generates a warning)

11. density.signature -> counts.signature

12. density.signature -> (counts, density) (generates an error)

Examples

# NOT RUN {
file <- system.file("extdata",
                    "strelka.regress.cat.sbs.96.csv",
                    package = "ICAMS")
if (requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5", quietly = TRUE)) {
  catSBS96.counts <- ReadCatalog(file, ref.genome = "hg19", 
                                 region = "genome",
                                 catalog.type = "counts")
  catSBS96.density <- TransformCatalog(catSBS96.counts,
                                       target.ref.genome = "hg19",
                                       target.region = "genome",
                                       target.catalog.type = "density")}
# }