,
Nanhai Jiang [aut] | Title: | Mutational Signatures from COSMIC (Catalogue of Somatic Mutations in Cancer) |
|---|---|
| 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. |
| Authors: | Steven Rozen [aut, cre] ,
Nanhai Jiang [aut] |
| Maintainer: | Steven Rozen <[email protected]> |
| License: | GPL-3 |
| Version: | 1.1.1 |
| Built: | 2025-02-10 05:00:27 UTC |
| Source: | https://github.com/rozen-lab/cosmicsig |
Mutational signatures data from COSMIC, Catalogue Of Somatic Mutations In Cancer (v3.0 - May 2019)
COSMIC_v3.0COSMIC_v3.0
A list with one element signature, with the
same structure as signature, except that
sub-element GRCh37 does contain SBS192.
The signatures are all genome signatures.
See CatalogRowOrder
in package ICAMS for the classification of mutation types.
https://cancer.sanger.ac.uk/signatures/.
sbs96_sig_v3.0 <- COSMIC_v3.0$signature$GRCh37$SBS96sbs96_sig_v3.0 <- COSMIC_v3.0$signature$GRCh37$SBS96
Mutational signatures data from COSMIC, Catalogue Of Somatic Mutations In Cancer (v3.1 - June 2020)
COSMIC_v3.1COSMIC_v3.1
A list with one element signature, with the
same structure as signature.
The signatures are all genome signatures.
See CatalogRowOrder
in package ICAMS for the classification of mutation types.
https://cancer.sanger.ac.uk/signatures/.
sbs96_sig_v3.1 <- COSMIC_v3.1$signature$GRCh37$SBS96sbs96_sig_v3.1 <- COSMIC_v3.1$signature$GRCh37$SBS96
Mutational signatures data from COSMIC, Catalogue Of Somatic Mutations In Cancer (v3.2 - March 2021)
COSMIC_v3.2COSMIC_v3.2
A list with two elements, signature and etiology.
signature is a list with the same structure as
signature.
etiology is a list with the same structure as
etiology.
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/
The signatures are all genome signatures.
See CatalogRowOrder
in package ICAMS for the classification of mutation types.
https://cancer.sanger.ac.uk/signatures/.
sbs96_sig_v3.2 <- COSMIC_v3.2$signature$GRCh37$SBS96sbs96_sig_v3.2 <- COSMIC_v3.2$signature$GRCh37$SBS96
Mutational signatures data from COSMIC, Catalogue Of Somatic Mutations In Cancer (v3.3 - June 2022)
COSMIC_v3.3COSMIC_v3.3
A list with two elements, signature and etiology.
signature is a list with the same structure as
signature.
etiology is a list with the same structure as
etiology.
The signatures are all genome signatures.
See CatalogRowOrder
in package ICAMS for the classification of mutation types.
https://cancer.sanger.ac.uk/signatures/.
sbs96_sig_v3.3 <- COSMIC_v3.3$signature$GRCh37$SBS96sbs96_sig_v3.3 <- COSMIC_v3.3$signature$GRCh37$SBS96
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.
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:
SBS (single base substitutions in the context of preceding and following bases, called SBS96 in this package)
DBS (doublet base substitutions, called DBS78 in this package)
ID (small insertions and deletions)
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.
https://cancer.sanger.ac.uk/signatures/.
List of mutational signatures's proposed etiology summarized from COSMIC, Catalogue Of Somatic Mutations In Cancer (v3.3 - June 2022)
etiologyetiology
A list with the elements:
SBS96
DBS78
ID
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.
https://cancer.sanger.ac.uk/signatures/.
sbs96_etiology <- etiology$SBS96sbs96_etiology <- etiology$SBS96
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.
get_etiology(mutation_type, sig_id)get_etiology(mutation_type, sig_id)
mutation_type |
Character string, one of "SBS96", "SBS192", "DBS78", "ID". |
sig_id |
Character vector with signature ids, e.g. |
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.
The etiology information is not versioned at the COSMIC website.
get_etiology(mutation_type = "ID", sig_id = c("ID1", "foo", "ID3"))get_etiology(mutation_type = "ID", sig_id = c("ID1", "foo", "ID3"))
Return a character vector of the names of possible SBS96 signature artifacts
possible_artifacts()possible_artifacts()
A character vector of the names of possible SBS96 signature artifacts.
artifact_sigs <- possible_artifacts()artifact_sigs <- possible_artifacts()
Return a character vector of the names of rare SBS96 signatures
rare_signatures()rare_signatures()
A character vector of the names of rare SBS96 signatures.
rare_sigs <- rare_signatures()rare_sigs <- rare_signatures()
"-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.
SBS96_ID_to_SBS192_ID(sig_ids)SBS96_ID_to_SBS192_ID(sig_ids)
sig_ids |
Character vector of SBS96 signature IDs. |
Character vector of corresponding SBS192 signature IDs; some have "-E" (for exome) post-pended.
sbs96_ids <- c("SBS1", "SBS23", "SBS25") sbs192_ids <- SBS96_ID_to_SBS192_ID(sbs96_ids)sbs96_ids <- c("SBS1", "SBS23", "SBS25") sbs192_ids <- SBS96_ID_to_SBS192_ID(sbs96_ids)
Mutational signatures data from COSMIC, Catalogue Of Somatic Mutations In Cancer (v3.3 - June 2022)
signaturesignature
A list with the following elements:
GRCh37: Homo sapiens (human) genome assembly GRCh37.
GRCh38: Homo sapiens (human) genome assembly GRCh38.
mm9: Mus musculus (house mouse) genome assembly mm9.
mm10: Mus musculus (house mouse) genome assembly mm10.
rn6: Rattus norvegicus (Norway rat) genome assembly rn6.
Each element contains the sub elements:
SBS96: Strand-agnostic single-base substitutions in trinucleotide context.
DBS78: Strand-agnostic doublet-base substitutions.
Element GRCh37 contains the additional sub elements:
ID: Strand-agnostic indels (short insertions and deletions).
The signatures are all genome signatures.
See CatalogRowOrder
in package ICAMS for the classification of mutation types.
https://cancer.sanger.ac.uk/signatures/.
sbs96_sig <- signature$GRCh37$SBS96sbs96_sig <- signature$GRCh37$SBS96