## ----style-knitr, eval=TRUE, echo=FALSE, results="asis"----------------------------- BiocStyle::latex() ## ----include=FALSE------------------------------------------------------------------ library(knitr) opts_chunk$set( concordance = TRUE, background = "#f3f3ff" ) ## ----req---------------------------------------------------------------------------- library("SparseSignatures") data(ssm560_reduced) head(ssm560_reduced) ## ----example_import----------------------------------------------------------------- library("BSgenome.Hsapiens.1000genomes.hs37d5") bsg = BSgenome.Hsapiens.1000genomes.hs37d5 data(mutation_categories) head(mutation_categories) ## ----example_import_not_eval,eval=FALSE--------------------------------------------- # imported_data = import.trinucleotides.counts(data=ssm560_reduced,reference=bsg,mutation_categories=mutation_categories) ## ----example_import_final_eveal----------------------------------------------------- data(imported_data) head(imported_data) ## ----image-1, fig.show='hide', fig.width=5, fig.height=5, results='hide'------------ patients.plot(trinucleotides_counts=imported_data,samples="PD10010a") ## ----patients_data------------------------------------------------------------------ data(patients) head(patients) ## ----starting_betas,eval=FALSE------------------------------------------------------ # starting_betas = startingBetaEstimation(x=patients,K=3:12,background_signature=background) ## ----lambda_range,eval=FALSE-------------------------------------------------------- # lambda_range = lambdaRangeBetaEvaluation(x=patients,K=10,beta=starting_betas[[8,1]], # lambda_values=c(0.05,0.10)) ## ----example_data------------------------------------------------------------------- data(starting_betas_example) data(lambda_range_example) ## ----cross_validation,eval=FALSE---------------------------------------------------- # cv = nmfLassoCV(x=patients,K=3:10) ## ----example_data_cv---------------------------------------------------------------- data(cv_example) ## ----best_configuation_signatures--------------------------------------------------- beta = starting_betas_example[["5_signatures","Value"]] res = nmfLasso(x = patients, K = 5, beta = beta, background_signature = background, seed = 12345) ## ----image-5, fig.show='hide', fig.width=5, fig.height=5, results='hide'------------ data(nmf_LassoK_example) signatures = nmf_LassoK_example$beta signatures.plot(beta=signatures, xlabels=FALSE) ## ----sessioninfo,results='asis',echo=FALSE------------------------------------------ toLatex(sessionInfo())