# #——消息= FALSE --------------------------------------------------------- 库(BRGenomics)数据(“PROseq”)(“txs_dm6_chr4”)txs_pr < -促进剂(txs_dm6_chr4 0 100 ) ## ---- 崩溃= TRUE --------------------------------------------------------- countmatrix_pr < - getCountsByPositions (PROseq、txs_pr ncores = 1)暗(countmatrix_pr)暗(countmatrix_pr) = = c(长度(txs_pr),独特的宽度(txs_pr ))) ## ----------------------------------------------------------------------------- 情节(x = 1: ncol (countmatrix_pr), y = colMeans (countmatrix_pr)类型=“l”,xlab =“距离TSS (bp)”,ylab = "意味着PRO-seq读取 ") ## ---- fig.height = 7, fig.width = 6 ----------------------------------------------- plot_meds < -函数(sig_thresh) {idx <——(rowSums (countmatrix_pr) > sig_thresh)情节(x = 1: ncol (countmatrix_pr), y =应用(countmatrix_pr idx,, 2,中位数),类型=“l”,主要= sprintf(“> % s读取的地区”,sig_thresh), xlab =“距离TSS (bp)”,ylab =“中间PRO-seq读”)}par (mfrow = c(3 2)),(我用c (0, 30 * 2 ^ (0:4))) {plot_meds (i ) } ## ----------------------------------------------------------------------------- bootmeans。df < - metaSubsample (PROseq、txs_pr binsize = 5,降低= 0.35,= 0.65,ncores = 1)头(bootmeans.df ) ## ----------------------------------------------------------------------------- 情节(意思是~ x, data = bootmeans。df, type = "l"， main = "PRO-seq信号"，ylim = c(0,1.4)， xlab = "距离TSS"， ylab = "平均信号+ 30% CI") #画一个多边形添加置信度带，#并使用adjustcolor()添加透明多边形(c(bootmeans. c))Df $x, rev(bootmeans. Df $x))， c(bootmeans. Df $x)。df美元低,转速(bootmeans.df上美元)),坳= adjustcolor(“黑色”,0.1),边界= FALSE ) ## ----------------------------------------------------------------------------- 需要(ggplot2) ggplot (bootmeans。df, aes (x,意味着))+ geom_line () + geom_ribbon (aes (x, ymin =低,ymax =上),α= 0.1)+实验室(title =“PRO-seq信号”,x =“TSS的距离”,y =”是指信号+ 30%可信区间”)+ theme_bw () ## ----------------------------------------------------------------------------- # 使ps_list < - 3数据集列表(ps1 = PROseq (seq(1、长度(PROseq), 3)], ps2 = PROseq (seq(2、长度(PROseq), 3)], ps3 = PROseq [seq(3、长度(PROseq),3 )]) ## ----------------------------------------------------------------------------- bm_list。df < - metaSubsample (ps_list、txs_pr binsize = 5,降低= 0.35,= 0.65,ncores = 1)头(bm_list.df ) ## ----------------------------------------------------------------------------- 需要(ggplot2) ggplot (bm_list。df, aes(x, mean, color = sample.name)) + geom_line() + geom_ribbon(aes(x, ymin = lower, ymax = upper, color = NULL, fill = sample.name)， alpha = 0.2) +实验室(title = "PRO-seq信号"，x = "距离TSS"， y = " mean信号+ 30% CI") + theme_bw()