sigstash makes it easy to load common mutational signature collections into R.
To visualise or simulate decompositions using these signatures, check out the sigverse
You can install the development version of sigstash from GitHub with:
# install.packages("devtools")
devtools::install_github("selkamand/sigstash")There are only 3 commands you need to know.
-
sig_availablewill list available signature collections -
sig_load('collection_name')will load the signature collection -
sig_load_annotations('collection_name')will load signature-level annotations (e.g. associated aetiologies)
library(sigstash)
sig_available()
#> # A tibble: 25 × 2
#> dataset description
#> <chr> <chr>
#> 1 REFSIG_v2.03_SBS Cancer-Related Single Base Substitution Signature…
#> 2 REFSIG_v2.03_DBS Cancer-Related Doublet Base Substitution Signatur…
#> 3 COSMIC_v3.4_SBS_GRCh38 Cancer-Related Single Base Substitution Signature…
#> 4 COSMIC_v3.4_DBS_GRCh38 Cancer-Related Doublet Base Substitution Signatur…
#> 5 COSMIC_v3.4_SV_GRCh38 Cancer-Related Structural Variant Signatures (GR…
#> 6 COSMIC_v3.4_CN_GRCh37 Cancer-Related CopyNumber Signatures (GRCh38). 48…
#> 7 COSMIC_v3.4_DBS_GRCh37 Cancer-Related Doublet Base Substitution Signatur…
#> 8 COSMIC_v3.4_ID_GRCh37 Cancer-Related Indel Signatures (GRCh37). 83 chan…
#> 9 COSMIC_v3.4_SBS_GRCh37 Cancer-Related Single Base Substitution Signature…
#> 10 COSMIC_v3.4_RNA-SBS_GRCh37 Cancer-Related Single Base Substitutions in RNA s…
#> # ℹ 15 more rows# Load Collection
cosmic_signatures <- sig_load("COSMIC_v3.3.1_SBS_GRCh38")
# Access a specific signature
cosmic_signatures[["SBS1"]]
#> # A tibble: 96 × 3
#> type channel fraction
#> <chr> <chr> <dbl>
#> 1 C>A A[C>A]A 0.000876
#> 2 C>A A[C>A]C 0.00222
#> 3 C>A A[C>A]G 0.000180
#> 4 C>A A[C>A]T 0.00127
#> 5 C>G A[C>G]A 0.00184
#> 6 C>G A[C>G]C 0.00119
#> 7 C>G A[C>G]G 0.000117
#> 8 C>G A[C>G]T 0.00113
#> 9 C>T A[C>T]A 0.0247
#> 10 C>T A[C>T]C 0.00615
#> # ℹ 86 more rowsSome signature collections will include signature level annotations for
example describing aetiologies typically associated with signatures.
These can be loaded using sig_load_annotations
sig_load_annotations("COSMIC_v3.3.1_SBS_GRCh38")
#> # A tibble: 79 × 14
#> signature class subclass aetiology aetiology_long comment SignatureVersion
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 SBS1 clock-l… clock-l… " Sponta… An endogenous… "Signa… Mutational Sign…
#> 2 SBS2 cytidin… cytidin… " APOBEC… Attributed to… "SBS2 … Mutational Sign…
#> 3 SBS3 dysfunc… HR " HR def… Defective hom… "SBS3 … Mutational Sign…
#> 4 SBS4 environ… tobacco " Aging … Associated wi… "Altho… Mutational Sign…
#> 5 SBS5 clock-l… clock-l… " Aging … Unknown. SBS5… "SBS5 … Mutational Sign…
#> 6 SBS6 dysfunc… MMR " MMR de… SBS6 is assoc… "SBS6 … Mutational Sign…
#> 7 SBS7a environ… UV " UV lig… SBS7a/SBS7b/S… "" Mutational Sign…
#> 8 SBS7b environ… UV " UV lig… SBS7a/SBS7b/S… "" Mutational Sign…
#> 9 SBS7c environ… UV " UV lig… SBS7a/SBS7b/S… "" Mutational Sign…
#> 10 SBS7d environ… UV " UV lig… SBS7a/SBS7b/S… "" Mutational Sign…
#> # ℹ 69 more rows
#> # ℹ 7 more variables: IdentificationStudy <chr>, IdentificationStudyURL <chr>,
#> # ExperimentalValidationStudy <chr>, ExperimentalValidationURL <chr>,
#> # ProposedAetiologySupport <chr>, ValidatedInOrthogonalTechniques <chr>,
#> # source.page <chr>