# #——load_style警告= FALSE,消息= FALSE,结果= "隐藏 "----------------- 库(BiocStyle) # #包,包括= FALSE -------------------------------------------------- 库(YAPSA)库(Biostrings)图书馆(BSgenome.Hsapiens.UCSC.hg19)图书馆(knitr) opts_chunk设置(echo = TRUE) opts_chunk设置美元(fig.show = '飞机 ') ## ---- loadStoredSigData ------------------------------------------------------- 数据(团体)的数据(达标)current_sig_df < - AlexInitialArtif_sig_df库(BSgenome.Hsapiens.UCSC.hg19 ) ## -----------------------------------------------------------------------------数据(“smallCellLungCancerMutCat_NatureGenetics2012 ") ## ---- loadLymphomaFtp eval = FALSE ---------------------------------------------- # smallCellLungCancer_NatureGenetics2012_ftp_path < - paste0(#“ftp://ftp.sanger.ac。英国癌症/ pub / / AlexandrovEtAl /”,#”somatic_mutation_data /肺小细胞”,# "肺小Cell_clean_somatic_mutations_for_signature_analysis.txt”)# exome_vcf_like_df < - # read.csv(文件= smallCellLungCancer_NatureGenetics2012_ftp_path # header = FALSE, 9 = \ t) #名称(exome_vcf_like_df) < - c(“PID”、“类型”、“铬”,“开始”,“停止”,“裁判”、“ALT”、“国旗”)# exome_vcf_like_df < -子集(exome_vcf_like_df、类型= =“潜艇”,#选择= c(铬、启动、裁判、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_cataloggue_from_df (# exome_vcf_like_df， # this_seqnames. #字段= "CHROM"， this_start。字段= "POS"， # this_end。字段= "POS"， this_PID。字段= "PID"， # this_subgroup。field = "SUBGROUP"， # this_refGenome = bsgenome . hspiens . ucsc。hg19,# this_wordLength = 3) # exome_mutCatRaw_df < - as.data.frame (exome_mutCatRaw_list矩阵美元)# #——loadCorrectionFactors ---------------------------------------------------- 数据(targetCapture_cor_factors) # #——listCorrectionFactors ---------------------------------------------------- 名(targetCapture_cor_factors) # #——correctTargetCapture ----------------------------------------------------- targetCapture < -“AgilentSureSelectAllExon cor_list < - targetCapture_cor_factors [[targetCapture]]corrected_catalog_df < - normalizeMotifs_otherRownames (exome_mutCatRaw_df cor_list rel_cor美元)# #——optimalCutoffs ----------------------------------------------------------- 数据(达标)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回声= FALSE ------------------------------------------ 帽< -“曝光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)