cosmicsig {cosmicsig}

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:

• 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.

Source

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