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.

1. sig_available will list available signature collections

2. sig_load('collection_name') will load the signature collection

3. sig_load_annotations('collection_name') will load signature-level annotations (e.g. associated aetiologies)

List available datasets

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 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>