CatalogRowOrder: Standard order of row names in a catalog
In steverozen/ICAMSxtra: ICAMSxtra
Description
Usage
Format
Note
Examples
Description
This data is designed for those
who need to create their own catalogs from formats not
supported by this package. The rownames denote the mutation
types. For example, for SBS96 catalogs, the rowname
AGAT represents a mutation from AGA > ATA.
Usage
1
Format
A list of character vectors indicating the standard
orders of row names in catalogs.
Note
In ID (small insertion and deletion) catalogs, deletion repeat sizes
range from 0 to 5+, but for plotting and end-user documentation deletion
repeat sizes range from 1 to 6+. In ID83 catalogs, deletion repeat sizes
range from 0 to 5.
Examples
1
2
3
4
5
6
catalog.row.order$ID115
# There are altogether 115 row names to denote the mutation types
# in ID115 catalog.
# The difference from the .$ID class in \code{\link{ICAMS::catalog.row.order}} is that
# single base nonhomopolymer indels have trinucleotide context added to them in the format
# INS/DEL:C/T:1:0_PF where P is the preceding base and F is the following base.
steverozen/ICAMSxtra documentation built on Feb. 9, 2022, 7:01 a.m.
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Description Usage Format Note Examples
Description
This data is designed for those who need to create their own catalogs from formats not supported by this package. The rownames denote the mutation types. For example, for SBS96 catalogs, the rowname AGAT represents a mutation from AGA > ATA.
Usage
1 |
Format
A list of character vectors indicating the standard orders of row names in catalogs.
Note
In ID (small insertion and deletion) catalogs, deletion repeat sizes range from 0 to 5+, but for plotting and end-user documentation deletion repeat sizes range from 1 to 6+. In ID83 catalogs, deletion repeat sizes range from 0 to 5.
Examples
1 2 3 4 5 6 | catalog.row.order$ID115
# There are altogether 115 row names to denote the mutation types
# in ID115 catalog.
# The difference from the .$ID class in \code{\link{ICAMS::catalog.row.order}} is that
# single base nonhomopolymer indels have trinucleotide context added to them in the format
# INS/DEL:C/T:1:0_PF where P is the preceding base and F is the following base.
|
R Package Documentation
Browse R Packages
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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