## ----eval=FALSE--------------------------------------------------------------- # if (!require("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("RESOLVE") ## ----message=FALSE------------------------------------------------------------ library("RESOLVE") data(ssm560_reduced) ## ----message=FALSE------------------------------------------------------------ library("BSgenome.Hsapiens.1000genomes.hs37d5") imported_data = getSBSCounts(data = ssm560_reduced, reference = BSgenome.Hsapiens.1000genomes.hs37d5) ## ----fig.width=7, fig.height=7, fig.cap="Visualization of the counts for patient PD10010a from the dataset published in Nik-Zainal, Serena, et al."---- patientsSBSPlot(trinucleotides_counts=imported_data,samples="PD10010a") ## ----eval=FALSE--------------------------------------------------------------- # data(background) # data(patients) # set.seed(12345) # res_denovo = signaturesDecomposition(x = patients, # K = 1:15, # background_signature = background, # nmf_runs = 100, # num_processes = 50) ## ----eval=FALSE--------------------------------------------------------------- # set.seed(12345) # res_cv = signaturesCV(x = patients, # beta = res_denovo$beta, # cross_validation_repetitions = 100, # num_processes = 50) ## ----------------------------------------------------------------------------- sessionInfo()