# #——loadStyle警告= FALSE,呼应= FALSE,消息= FALSE,结果=“隐藏”——图书馆(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 ') ## ---- loadPCAWGsigs ------------------------------------------------------------ 数据(sigs_pcawg) # #——captionSpectra,echo=FALSE----------------------------------------------- cap <-": Indel标记ID3的核苷酸交换光谱，与吸烟有关，ID6的核苷酸交换光谱，与同源重组修复缺陷有关。"# #——INDELsigExample,包括= TRUE, fig.width = 15, fig.height = 6, fig.cap =帽——plotExchangeSpectra_indel (PCAWG_SP_ID_sigs_df [c(3、6 )]) ## ---- INDELsigInfo ------------------------------------------------------------- current_caption < - paste0 (Indel突变信息签名。)如果(!(“repress_tables”)存在kable (PCAWG_SP_ID_sigInd_df row.names = FALSE,标题= current_caption) # #——loadGoNL ----------------------------------------------------------------- 数据(GenomeOfNl_raw) GenomeOfNl_raw < - GenomeOfNl_raw [c(1、2、4、5 )] ## ---- loadGoNLraw -------------------------------------------------------------- load_data_new < -假如果(load_data_new){数据< data.frame(矩阵(ncol = 8,Nrow = 0)) for(index in seq_along(1:22)){print(index) temp <- tempfile() file_path <- paste0("https://molgenis26.target.rug.nl/ downloads/gonl_public/ variables /release5/ gonl. zip (")Chr "， index， ".snps_indels.r5.vcf.gz")下载。文件(file_path, temp)数据<- rbind(数据，读取。表(gzfile(临时paste0(“gonl。空空”,指数,“.snps_indels.r5.vcf”)),头= FALSE, 9 = " \ t”,stringsAsFactors = FALSE) < -数据(grep(“INDEL”,数据V8美元),)分开(临时)}colnames(数据)< - c(“铬”、“POS”、“ID”,“裁判”、“ALT”、“定性”,“过滤器”,“信息”)GenomeOfNl_raw < -数据(c(1、2、4、5 )] } ## ---- showsTopOfDf,回声= FALSE ------------------------------------------------- kable(头(GenomeOfNl_raw),标题= "的VCF文件包含GoNL INDEL数据 ") ## ---- randomizeDataSet,warning= FALSE----------------------------------------- seed= 2 set.seed(seed) number_of_indels <- sample(c(30:70)， 15, replace = TRUE) index=0 seed=3 set.seed(seed) vcf_like_indel_lists <- lapply(number_of_indels, function(size){df_per_PID <- GenomeOfNl_raw[sample(nrow(GenomeOfNl_raw)， size, replace = FALSE)，] index <<- index+1 df_per_PID$PID <- rep(paste0("PID_"， index)，length(size)) df_pid <- df_per_PID[order(df_per_PID$CHROM)，] return(df_pid)}) vcf_like_indel_df <- do.call(rbind.data.frame, vcf_like_indel_lists) kable(head(vcf_like_indel_df)，标题=" vcf_like_df的头部包含subsampled GoNL Indel数据")## ----createMutationalCatalog，警告= FALSE ----------------------------------- vcf_like_indel_trans_df < - translate_to_hg19 (vcf_like_indel_df,“铬”)mutational_cataloge_indel_df < - create_indel_mutation_catalogue_from_df (in_dat = vcf_like_indel_trans_df in_signature_df = PCAWG_SP_ID_sigs_df) kable(头(mutational_cataloge_indel_df [1:5 ])) ## ---- loadCutoffs,警告= FALSE ----------------------------------------------- 数据(cutoffs_pcawg) # #——LCDdecompostion,warning=FALSE------------------------------------------- current_cataloggue_df <- mutational_catalogge_indel_df current_sig_df <- pcawg_sp_id_sigs_pid_df current_cutoff_pid_vector <- cutoffPCAWG_ID_WGS_Pid_df[3，] current_sigInd_df <- PCAWG_SP_ID_sigInd_df current_LCDlistsList <- LCD_complex_cutoff_combined(current_cataloggue_df, current_sig_df, in_cutoff_vector = current_cutoff_pid_vector, in_filename = NULL, in_method = "abs"， in_sig_ind_df = current_sigInd_df) current_consensus_LCDlist <- current_LCDlistsList$consensus if(!exists("repress_tables")) as.character(current_consensus_LCDlist$out_sig_ind_df$sig) ## ----captionExposure, echo=FALSE---------------------------------------------- cap <- ":Exposures to Indel mutational signatures in the artificial data created by sampling GoNL variants. Exposures were obtained from a decomposition with PCAWG Indel signatures as well as their signature specific-cutoffs (cutoffPCAWG_ID_WGS_Pid_df)." ## ----plotExposure, echo=TRUE, warning=FALSE, fig.width=15, fig.height=6, fig.cap= cap---- exposures_barplot(current_LCDlistsList$perPID$exposures, current_LCDlistsList$perPID$out_sig_ind_df) ## ----captionCI, echo=FALSE---------------------------------------------------- cap <- "Confidence interval calculation for exposures to Indel mutational signatures" ## ----CI, echo=TRUE, warning=FALSE, fig.width=17, fig.height=15, fig.cap=cap---- confidence_intervals_ID <- confidence_indel_only_calulation( in_current_indel_df = current_catalogue_df) plot(confidence_intervals_ID$p_complete_PCAWG_ID)