## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----Load, message=FALSE------------------------------------------------------ library(SigsPack) ## ----------------------------------------------------------------------------- if (require(BSgenome.Hsapiens.UCSC.hg19)) { sample <- vcf2mut_cat( system.file("extdata", "example.vcf.gz", package="SigsPack"), BSgenome.Hsapiens.UCSC.hg19 ) } ## ----------------------------------------------------------------------------- data("cosmicSigs") cats <- create_mut_catalogues(10, 500, P=cosmicSigs, sig_set = c(2,6,15,27)) knitr::kable(head(cats[['catalogues']])) ## ----------------------------------------------------------------------------- reps <- bootstrap_mut_catalogues(n = 1000, original = cats[["catalogues"]][,1]) # using only signatures 4, 17, 23 and 30 for signature estimation sigs <- signature_exposure(reps, sig_set = c(4,17,23,30)) print(sigs$exposures[,1]) ## ----fig.show='hold', fig.height=7, fig.width=7------------------------------- report <- summarize_exposures(reps[,1]) knitr::kable( head(report) ) ## ----------------------------------------------------------------------------- if (require(BSgenome.Hsapiens.UCSC.hg19)){ genome_contexts <- get_context_freq(BSgenome.Hsapiens.UCSC.hg19) exome_contexts <- get_context_freq( BSgenome.Hsapiens.UCSC.hg19, system.file("extdata", "example.bed.gz", package="SigsPack") ) normalized_mut_cat <- SigsPack::normalize(sample, exome_contexts, hg19context_freq) } ## ----fig.show='hold', fig.height=7, fig.width=7------------------------------- if (require(BSgenome.Hsapiens.UCSC.hg19)) { sigs_norm <- signature_exposure(sum(sample) * normalized_mut_cat) report_norm <- summarize_exposures(normalized_mut_cat, m=sum(sample)) reps_norm <- bootstrap_mut_catalogues( n=1000, original=normalized_mut_cat, m=sum(sample) ) } ## ----------------------------------------------------------------------------- sessionInfo()