# #设置,包括= FALSE --------------------------------------------------- 库(DegNorm) knitr: opts_chunk美元集(崩溃= TRUE,发表评论 = "#>" ) 图书馆(knitr)美元knit_hooks组(optipng = hook_optipng) # # - eval = FALSE --------------------------------------------------------------- # 如果(!requireNamespace(“BiocManager”,悄悄地= TRUE)) # install.packages (BiocManager) # BiocManager::安装(“DegNorm ") ## ----------------------------------------------------------------------------- ## 指定从RNA-seq bam_files,你应该通过自己的bam文件替换bam_file_list = list.files (path =执行(“extdata”,包=“DegNorm”),模式=本”美元,full.names = TRUE ) ## ----------------------------------------------------------------------------- ## gtf_file你用于RNA-seq对齐,换成自己的gtf文件gtf_file = list.files (path =执行(“extdata”,包=“DegNorm”),模式=“.gtf”美元,full.names = TRUE) # # - eval = TRUE ---------------------------------------------------------------- ## 计算所有样本的阅读分数为所有报道基因coverage_res_chr21_sub = read_coverage_batch (bam_file_list,gtf_file核心= 2)# # - eval = FALSE --------------------------------------------------------------- # ## 保存覆盖率结果#保存(coverage_res_chr21_sub、文件= " coverage_res_chr21_sub.Rda ") ## ----------------------------------------------------------------------------- 数据(“coverage_res_chr21”)# #总结报道结果summary_CoverageClass (coverage_res_chr21 ) ## ----------------------------------------------------------------------------- ## 提取报道分数和计数从coverage_res coverage_matrix = coverage_res_chr21覆盖数= coverage_res_chr21计数# #美元——eval = TRUE ---------------------------------------------------------------- res_DegNorm_chr21 = degnorm (read_coverage = coverage_res_chr21[[1]],数= coverage_res_chr21[[2]],迭代= 5,down_sampling = 1, grid_size = 10,循环= 100,核= 2)# #——eval = FALSE --------------------------------------------------------------- # ## 保存DegNorm结果#保存(res_DegNorm_chr21文件= " res_DegNorm_chr21.Rda ") ## ----------------------------------------------------------------------------- 数据(“res_DegNorm_chr21 ") ## ----------------------------------------------------------------------------- ## 摘要DegNorm输出summary_DegNormClass (res_DegNorm_chr21) # #----------------------------------------------------------------------------- ## extrac规范化读计数counts_normed = res_DegNorm_chr21 counts_normed # #——fig.width = 5美元,无花果。身高= 4,消息= FALSE, eval = TRUE ------------------------- ## 基因命名为“SOD1”plot_coverage (gene_name =“SOD1 coverage_output = coverage_res_chr21 degnorm_output = res_DegNorm_chr21组= c (0, 1, 1 )) ## ---- fig.width = 5,无花果。height=4,message=FALSE,eval=TRUE------------------------- ##基因命名为“SOD1”plot_coverage(gene_name=“SOD1”，coverage_output=coverage_res_chr21, degnorm_output=res_DegNorm_chr21,group=c(0,1)， samples=c("SRR873822_chr21. sh)。bam”、“SRR873834_chr21.bam ")) ## ---- fig.width = 5,无花果。height=4,message=FALSE,warning=FALSE,eval=TRUE----------- plot_boxplot(DI=res_DegNorm_chr21$DI) ## ----fig.width=5，图。身高= 4,消息= FALSE, eval = TRUE ------------------------- plot_heatmap (DI = res_DegNorm_chr21 $ DI) # #——fig.width = 5,无花果。height=4,message=FALSE,warning=FALSE,eval=TRUE----------- plot_corr(DI=res_DegNorm_chr21$DI) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()