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_available
will 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: 8 × 2
#> dataset description
#> <chr> <chr>
#> 1 COSMIC_v3.3.1_SBS_GRCh38 Cancer-Related Single Base Substitution Signatures (…
#> 2 COSMIC_v3.3_DBS_GRCh38 Cancer-Related Doublet Base Substitution Signatures …
#> 3 COSMIC_v3.3_ID_GRCh37 Cancer-Related Indel Signatures (GRCh37). 83 channel…
#> 4 COSMIC_v3.3_CN_GRCh37 Cancer-Related CopyNumber Signatures (GRCh37). 48 ch…
#> 5 COSMIC_v3.3.1_SBS_GRCh37 Cancer-Related Single Base Substitution Signatures (…
#> 6 COSMIC_v3.3_DBS_GRCh37 Cancer-Related Doublet Base Substitution Signatures …
#> 7 COSMIC_v2_SBS_GRCh38 An older set of cancer-related Single Base Substitut…
#> 8 COSMIC_v2_SBS_GRCh37 An older set of cancer-related Single Base Substitut…
# 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 rows
Some 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>