## ----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) head(imported_data) ## ----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") ## ----------------------------------------------------------------------------- data(background) data(patients) set.seed(12345) res_denovo = signaturesDecomposition(x = patients[1:3,], K = 3:4, background_signature = background, nmf_runs = 2, sparsify = FALSE, num_processes = 1) ## ----------------------------------------------------------------------------- set.seed(12345) res_cv = signaturesCV(x = patients[1:3,], beta = res_denovo$beta, cross_validation_iterations = 2, cross_validation_repetitions = 2, num_processes = 1) ## ----fig.width=7, fig.height=7, fig.cap="Visualization of the discovered signatures."---- signatures = res_denovo$beta[[2]] signaturesSBSPlot(beta=signatures, xlabels=FALSE) ## ----------------------------------------------------------------------------- sessionInfo()