Title: Mutational Signatures from COSMIC (Catalogue of Somatic Mutations in Cancer)
Version: 1.1.1
Description: A data package with 2 main package variables: 'signature' and 'etiology'. The 'signature' variable contains the latest mutational signature profiles released on COSMIC https://cancer.sanger.ac.uk/signatures/ for 3 mutation types: * Single base substitutions in the context of preceding and following bases, * Doublet base substitutions, and * Small insertions and deletions. The 'etiology' variable provides the known or hypothesized causes of signatures. 'cosmicsig' stands for COSMIC signatures. Please run ?'cosmicsig' for more information.
License: GPL-3
URL: https://github.com/Rozen-Lab/cosmicsig
BugReports: https://github.com/Rozen-Lab/cosmicsig/issues
Language: en-US
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.3
Depends: R (≥ 3.5)
Suggests: testthat (≥ 3.0.0), ICAMS, usethis
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2023-08-30 06:49:49 UTC; User
Author: Steven Rozen ORCID iD [aut, cre], Nanhai Jiang ORCID iD [aut]
Maintainer: Steven Rozen <steverozen@pm.me>
Repository: CRAN
Date/Publication: 2023-08-30 08:20:02 UTC

cosmicsig: A package of mutational signatures from COSMIC (Catalogue Of Somatic Mutations In Cancer) https://cancer.sanger.ac.uk/signatures/.

Description

For a general introduction to mutational signatures and the techniques used to discover them, see Alexandrov et al., 2020 doi:10.1038/s41586-020-1943-3.

Details

This is a data package with 2 main package variables: signature and etiology.

The signature variable contains the latest mutational signature profiles released on https://cancer.sanger.ac.uk/signatures/ for 3 mutation types:

The package variable etiology contains information on known or hypothesized causes of mutational signatures. In general, it is better to use get_etiology.

Earlier releases are available in the variables COSMIC_version, e.g. COSMIC_v3.2.

The profiles of SBSs signatures depend on the frequencies of trinucleotides in a genome and profiles of DBS signatures depend on the frequencies of dinucleotides in a genome. Therefore COSMIC and this package provide slightly different signatures for different reference genomes. COSMIC and this package offer versions of SBS and DBS signatures for human GRCh37 (also known as hg19) and GRCh38, and for mouse and rat. ID signatures do not take into consideration differing nucleotide composition between reference genomes because relating this to the ID mutational categories would be extremely complicated.

Some signatures are due to experimental or laboratory artifacts. Function possible_artifacts returns these.

Source

https://cancer.sanger.ac.uk/signatures/.

Mutational signatures data from COSMIC, Catalogue Of Somatic Mutations In Cancer (v3.0 - May 2019)

Description

Mutational signatures data from COSMIC, Catalogue Of Somatic Mutations In Cancer (v3.0 - May 2019)

Usage

COSMIC_v3.0

Format

A list with one element signature, with the same structure as signature, except that sub-element GRCh37 does contain SBS192.

Remark

The signatures are all genome signatures.
See CatalogRowOrder in package ICAMS for the classification of mutation types.

Source

https://cancer.sanger.ac.uk/signatures/.

Examples

sbs96_sig_v3.0 <- COSMIC_v3.0$signature$GRCh37$SBS96

Mutational signatures data from COSMIC, Catalogue Of Somatic Mutations In Cancer (v3.1 - June 2020)

Description

Mutational signatures data from COSMIC, Catalogue Of Somatic Mutations In Cancer (v3.1 - June 2020)

Usage

COSMIC_v3.1

Format

A list with one element signature, with the same structure as signature.

Remark

The signatures are all genome signatures.
See CatalogRowOrder in package ICAMS for the classification of mutation types.

Source

https://cancer.sanger.ac.uk/signatures/.

Examples

sbs96_sig_v3.1 <- COSMIC_v3.1$signature$GRCh37$SBS96

Mutational signatures data from COSMIC, Catalogue Of Somatic Mutations In Cancer (v3.2 - March 2021)

Description

Mutational signatures data from COSMIC, Catalogue Of Somatic Mutations In Cancer (v3.2 - March 2021)

Usage

COSMIC_v3.2

Format

A list with two elements, signature and etiology.

Note

SBS10c, SBS10d, SBS91, SBS92, SBS93, SBS94 (total 6) new SBS signatures were added in COSMIC v3.2. See the news from COSMIC release for more details https://cosmic-blog.sanger.ac.uk/cosmic-mutational-signatures-release-v3-2/

Remark

The signatures are all genome signatures.
See CatalogRowOrder in package ICAMS for the classification of mutation types.

Source

https://cancer.sanger.ac.uk/signatures/.

Examples

sbs96_sig_v3.2 <- COSMIC_v3.2$signature$GRCh37$SBS96

Mutational signatures data from COSMIC, Catalogue Of Somatic Mutations In Cancer (v3.3 - June 2022)

Description

Mutational signatures data from COSMIC, Catalogue Of Somatic Mutations In Cancer (v3.3 - June 2022)

Usage

COSMIC_v3.3

Format

A list with two elements, signature and etiology.

Remark

The signatures are all genome signatures.
See CatalogRowOrder in package ICAMS for the classification of mutation types.

Source

https://cancer.sanger.ac.uk/signatures/.

Examples

sbs96_sig_v3.3 <- COSMIC_v3.3$signature$GRCh37$SBS96

Translate SBS96 signature IDs to SBS192 signature IDs by adding "-E" if necessary

Description

"-E" added to the name of a transcriptional strand bias signature indicates that it was extracted only from exome sequencing data, and thus reflects transcriptional strand bias in the exome rather than in the entire transcript, including introns.

Usage

SBS96_ID_to_SBS192_ID(sig_ids)

Arguments

sig_ids

Character vector of SBS96 signature IDs.

Value

Character vector of corresponding SBS192 signature IDs; some have "-E" (for exome) post-pended.

Examples

sbs96_ids <- c("SBS1", "SBS23", "SBS25")
sbs192_ids <- SBS96_ID_to_SBS192_ID(sbs96_ids)

List of mutational signatures's proposed etiology summarized from COSMIC, Catalogue Of Somatic Mutations In Cancer (v3.3 - June 2022)

Description

List of mutational signatures's proposed etiology summarized from COSMIC, Catalogue Of Somatic Mutations In Cancer (v3.3 - June 2022)

Usage

etiology

Format

A list with the elements:

Each element is a single-column matrix with rownames being the signature IDs and values being a short string describing the proposed etiology.

In general use get_etiology, which handles new signatures do not have an element in etiology.

Source

https://cancer.sanger.ac.uk/signatures/.

Examples

sbs96_etiology <- etiology$SBS96

Get the proposed etiology of mutational signatures.

Description

Return the known or hypothesized causes of mutational signatures. The level of evidence supporting the proposed etiologies varies. In addition, some proposed etiologies are more akin to associations than specific, mechanistic causes.

Usage

get_etiology(mutation_type, sig_id)

Arguments

mutation_type

Character string, one of "SBS96", "SBS192", "DBS78", "ID".

sig_id

Character vector with signature ids, e.g. c("SBS3", "SBS5").

Value

A character vector of the same length as sig_id, each element of which is the etiology of the corresponding signature, if available, or else the empty string.

Note

The etiology information is not versioned at the COSMIC website.

See Also

get_etiology

Examples

get_etiology(mutation_type = "ID", sig_id = c("ID1", "foo", "ID3"))

Return a character vector of the names of possible SBS96 signature artifacts

Description

Return a character vector of the names of possible SBS96 signature artifacts

Usage

possible_artifacts()

Value

A character vector of the names of possible SBS96 signature artifacts.

Examples

artifact_sigs <- possible_artifacts()

Return a character vector of the names of rare SBS96 signatures

Description

Return a character vector of the names of rare SBS96 signatures

Usage

rare_signatures()

Value

A character vector of the names of rare SBS96 signatures.

Examples

rare_sigs <- rare_signatures()

Mutational signatures data from COSMIC, Catalogue Of Somatic Mutations In Cancer (v3.3 - June 2022)

Description

Mutational signatures data from COSMIC, Catalogue Of Somatic Mutations In Cancer (v3.3 - June 2022)

Usage

signature

Format

A list with the following elements:

Each element contains the sub elements:

Element GRCh37 contains the additional sub elements:

Remark

The signatures are all genome signatures.
See CatalogRowOrder in package ICAMS for the classification of mutation types.

Source

https://cancer.sanger.ac.uk/signatures/.

Examples

sbs96_sig <- signature$GRCh37$SBS96