library(sigminer)data("simulated_catalogs")mat<-t(simulated_catalogs$set1)mat[1:5,1:5]#>          A[C>A]A A[C>A]C A[C>A]G A[C>A]T C[C>A]A#> Sample_1     911     761      88     744     883#> Sample_2     195     175      19     174     225#> Sample_3      95      51      12      55     142#> Sample_4     131      71      14      77     170#> Sample_5      33      10       2      14      55

# Here I reduce the values for n_bootstrap and n_nmf_run for reducing the run time.  In practice,# you should keep default or increase the values for better estimation.  The input data here is# simulated from 10 mutational signaturese1<-bp_extract_signatures(mat,range =8:12,n_bootstrap =5,n_nmf_run =10)

bp_show_survey2(e1,highlight =10)#> Variables can be used: signature_number, silhouette, sample_cosine_distance, L1_error, L2_error, exposure_positive_correlation, signature_similarity_within_cluster, signature_similarity_across_cluster, silhouette_sample

obj<-bp_get_sig_obj(e1,10)

show_sig_profile(obj,mode ="SBS",style ="cosmic")

show_sig_exposure(obj,rm_space =TRUE)

sim<-get_sig_similarity(obj,sig_db ="SBS")#> -Comparing against COSMIC signatures#> ------------------------------------#> --Found Sig1 most similar to SBS12#>    Aetiology: Unknown [similarity: 0.932]#> --Found Sig2 most similar to SBS13#>    Aetiology: Activity of APOBEC family of cytidine deaminases [similarity: 0.97]#> --Found Sig3 most similar to SBS5#>    Aetiology: Unknown (clock-like signature) [similarity: 0.95]#> --Found Sig4 most similar to SBS3#>    Aetiology: Defective homologous recombination DNA damage repair [similarity: 0.927]#> --Found Sig5 most similar to SBS8#>    Aetiology: Unknown [similarity: 0.934]#> --Found Sig6 most similar to SBS18#>    Aetiology: Damage by reactive oxygen species [similarity: 0.975]#> --Found Sig7 most similar to SBS1#>    Aetiology: Spontaneous deamination of 5-methylcytosine (clock-like signature) [similarity: 0.76]#> --Found Sig8 most similar to SBS6#>    Aetiology: Defective DNA mismatch repair [similarity: 0.957]#> --Found Sig9 most similar to SBS17b#>    Aetiology: Unknown [similarity: 0.888]#> --Found Sig10 most similar to SBS2#>    Aetiology: Activity of APOBEC family of cytidine deaminases [similarity: 0.986]#> ------------------------------------#> Return result invisiblely.

if (require(pheatmap)) {    pheatmap::pheatmap(sim$similarity)}

QA

If you encounter warnings aboutfuture package, pleaseset the following options before running code:

options(future.rng.onMisuse ="ignore",future.globals.maxSize =Inf)

More

Please go toreferencelist for well organized functions and documentation.

For more about mutational signature andsigminerusage, you can readsigminer-book.