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ICAMS (version 2.0.7)

CollapseCatalog: "Collapse" a catalog.

Description

  1. Take a mutational spectrum or signature catalog that is based on a fined-grained set of features (for example, single-nucleotide substitutions in the context of the preceding and following 2 bases).

  2. Collapse it to a catalog based on a coarser-grained set of features (for example, single-nucleotide substitutions in the context of the immediately preceding and following bases).

Collapse192CatalogTo96 Collapse an SBS 192 catalog to an SBS 96 catalog.

Collapse1536CatalogTo96 Collapse an SBS 1536 catalog to an SBS 96 catalog.

Collapse144CatalogTo78 Collapse a DBS 144 catalog to a DBS 78 catalog.

Usage

Collapse192CatalogTo96(catalog)
Collapse1536CatalogTo96(catalog)
Collapse144CatalogTo78(catalog)

Arguments

catalog

A catalog as defined in ICAMS.

Value

A catalog as defined in ICAMS.

Examples

Run this code
# NOT RUN {
# Create an SBS192 catalog and collapse it to an SBS96 catalog
object <- matrix(1, nrow = 192, ncol = 1, 
                 dimnames = list(catalog.row.order$SBS192))
catSBS192 <- as.catalog(object, ref.genome = "hg19", region = "transcript")
catSBS96 <- Collapse192CatalogTo96(catSBS192)
# }

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