df < - read.table(“我。床”,9 = " \ t”)colnames (df) < - c(“铬”、“开始”、“结束”)df < - read.table(“我。colnames(df) <- c(“chr”，“start”，“end”)library(RangesTutorial2017)调用<- readVcf(system。extdata ("extdata . txt "， "lumpy.vcf.gz"， package="RangesTutorial2017")) true <- readVcf(system. txt ")文件(“extdata”、“truth.vcf。<-子集(调用，SVTYPE=="DEL")调用<-子集(调用，SVTYPE=="DEL") seqlevelsStyle(调用)<- "NCBI"真理<- keepstandard染色体(真理，剪接.mode="粗")调用<- as(调用，"VRanges")真理<- as(真理，"VRanges")VRanges)裁判(真理)< -“。”裁判(真理)< -“。”调用< -调用(称为(调用)]点击< - findOverlaps(真理,调用)点击< - findOverlaps(真理,调用)点击<——(点击,“列表”)call_rl < - extractList(范围(调用),点击)dev < - abs(开始(真理)——开始(call_rl)) + abs(端(真理)-端(call_rl)) dev_ord < -订单(dev)保持< phead (dev_ord,rdf <- as.data.frame(truth) ggplot(aes(x=deviance)， data=子集(rdf, deviance <= 500)) + stat_ecdf() + ylab("fraction <= deviance") truth$called <- with(truth，is.na(deviance) & deviance <= 300) mean(TRUE $called)调用$fp <- TRUE调用$fp[子集(TRUE, called)$call] <- FALSE mean(调用$fp) file <- system。- import(file) seqlevelsStyle(altRegions) <- "NCBI" altRegions <- keepstandardtechnologies (altRegions, pruning.mode="coarse")调用$inAlt <-调用%over% altRegions xtabs(~ inAlt + fp，调用)