CollapseCatalog: "Collapse" a catalog
In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')
Description
Usage
Arguments
Value
Examples
Description
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).
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
1
2
3
4
5
Collapse192CatalogTo96(catalog)
Collapse1536CatalogTo96(catalog)
Collapse144CatalogTo78(catalog)
Arguments
catalog
A catalog as defined in ICAMS.
Value
A catalog as defined in ICAMS.
Examples
1
2
3
4
5
# Create an SBS192 catalog and collapse it to an SBS96 catalog
object <- matrix(1, nrow = 192, ncol = 1,
dimnames = list(catalog.row.order$SBS192))
catSBS192 <- as.catalog(object, region = "transcript")
catSBS96 <- Collapse192CatalogTo96(catSBS192)
ICAMS documentation built on April 3, 2021, 5:07 p.m.
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Description Usage Arguments Value Examples
Description
Take a mutational spectrum or signature catalog that is based on a fined-grained set of features (for example, single-nucleotide substitutions in the context of the preceding and following 2 bases).
Collapse it to a catalog based on a coarser-grained set of features (for example, single-nucleotide substitutions in the context of the immediately preceding and following bases).
Collapse192CatalogTo96 Collapse an SBS 192 catalog
to an SBS 96 catalog.
Collapse1536CatalogTo96 Collapse an SBS 1536 catalog
to an SBS 96 catalog.
Collapse144CatalogTo78 Collapse a DBS 144 catalog
to a DBS 78 catalog.
Usage
1 2 3 4 5 | Collapse192CatalogTo96(catalog)
Collapse1536CatalogTo96(catalog)
Collapse144CatalogTo78(catalog)
|
Arguments
catalog |
A catalog as defined in |
Value
A catalog as defined in ICAMS.
Examples
1 2 3 4 5 | # Create an SBS192 catalog and collapse it to an SBS96 catalog
object <- matrix(1, nrow = 192, ncol = 1,
dimnames = list(catalog.row.order$SBS192))
catSBS192 <- as.catalog(object, region = "transcript")
catSBS96 <- Collapse192CatalogTo96(catSBS192)
|
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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