## ----load_style, warning=FALSE, message=FALSE, results="hide"----------------- library(BiocStyle) ## ----packages, include=FALSE-------------------------------------------------- library(YAPSA) library(Biostrings) library(BSgenome.Hsapiens.UCSC.hg19) library(knitr) opts_chunk$set(echo=TRUE) opts_chunk$set(fig.show='asis') ## ---- loadStoredSigData------------------------------------------------------- data(sigs) data(cutoffs) current_sig_df <- AlexInitialArtif_sig_df library(BSgenome.Hsapiens.UCSC.hg19) ## ----------------------------------------------------------------------------- data("smallCellLungCancerMutCat_NatureGenetics2012") ## ----loadLymphomaFtp, eval=FALSE---------------------------------------------- # smallCellLungCancer_NatureGenetics2012_ftp_path <- paste0( # "ftp://ftp.sanger.ac.uk/pub/cancer/AlexandrovEtAl/", # "somatic_mutation_data/Lung Small Cell/", # "Lung Small Cell_clean_somatic_mutations_for_signature_analysis.txt") # exome_vcf_like_df <- # read.csv(file = smallCellLungCancer_NatureGenetics2012_ftp_path, # header=FALSE,sep="\t") # names(exome_vcf_like_df) <- c("PID","TYPE","CHROM","START", # "STOP","REF","ALT","FLAG") # exome_vcf_like_df <- subset(exome_vcf_like_df, TYPE == "subs", # select = c(CHROM, START, REF, ALT, PID)) # names(exome_vcf_like_df)[2] <- "POS" # exome_vcf_like_df <- translate_to_hg19(exome_vcf_like_df,"CHROM") # word_length <- 3 # exome_mutCatRaw_list <- # create_mutation_catalogue_from_df( # exome_vcf_like_df, # this_seqnames.field = "CHROM", this_start.field = "POS", # this_end.field = "POS", this_PID.field = "PID", # this_subgroup.field = "SUBGROUP", # this_refGenome = BSgenome.Hsapiens.UCSC.hg19, # this_wordLength = 3) # exome_mutCatRaw_df <- as.data.frame(exome_mutCatRaw_list$matrix) ## ----loadCorrectionFactors---------------------------------------------------- data(targetCapture_cor_factors) ## ----listCorrectionFactors---------------------------------------------------- names(targetCapture_cor_factors) ## ----correctTargetCapture----------------------------------------------------- targetCapture <- "AgilentSureSelectAllExon" cor_list <- targetCapture_cor_factors[[targetCapture]] corrected_catalog_df <- normalizeMotifs_otherRownames(exome_mutCatRaw_df, cor_list$rel_cor) ## ----optimalCutoffs----------------------------------------------------------- data(cutoffs) current_cutoff_vector <- cutoffCosmicValid_rel_df[6,] ## ----LCDwithCutoffs----------------------------------------------------------- exome_listsList <- LCD_complex_cutoff_combined( in_mutation_catalogue_df = corrected_catalog_df, in_cutoff_vector = current_cutoff_vector, in_signatures_df = AlexCosmicValid_sig_df, in_sig_ind_df = AlexCosmicValid_sigInd_df) ## ----ExposuresCutoffsCap, echo=FALSE------------------------------------------ cap <- "Exposures barplot." ## ----exposuresCutoffs, warning=FALSE, fig.width=8, fig.height=6, fig.cap=cap---- exposures_barplot( in_exposures_df = exome_listsList$cohort$exposures, in_signatures_ind_df = exome_listsList$cohort$out_sig_ind_df)