sigstash

sigstash makes it easy to load common mutational signature collections into R.

To visualise or simulate decompositions using these signatures, check out the sigverse

Installation

You can install the development version of sigstash from GitHub with:

# install.packages("devtools")
devtools::install_github("selkamand/sigstash")

Quick Start

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)

List available datasets

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 and Visualise datasets

# 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

Load signature metadata

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>