## ----设置，包括= false -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- knitr::opts_chunk$set(echo = TRUE, eval = FALSE, warning = FALSE, error = FALSE) ## ------------------------------------------------------------------------------------------------------------------＃p1 <-granges（“ 1”，iranges（c（1，4，7），宽度= 2））＃p2 <-granges（“ 1）“，iranges（c（2，5），宽度= 3））＃ol_min < - findoverlapsofpeaks（p1，p2，connectectedPeaks =“ min”）＃## ## ## counts将是那组＃##的最小峰值连接的峰，因此您将获得2。＃ol_merge < - findoverlapsofpeaks（p1，p2，connectedpeaks =“ merge”）＃## ##每组连接峰值＃ol_min $ venn_cnt $ venn_cnt＃ol_merge--------------------------------------------------------------------------------------------------------------------------＃图书馆（Chippeakanno）＃bed <-System.file（“ Extdata”，“ Macs_output.bed”，package = =“ chippeakanno”）＃gr1 < - togranges（bed，format =“ bed”，header = false）＃gff <-system.file（“ extdata”，“ gff_peaks.gff”，package =“ chippeakanno”）＃gr2 < - gr2 < -togranges（gff，format =“ gff”，header = false，skip = 3）＃ol < - findoverlapsofpeaks（gr1，gr2）＃peadNames <-ol $ peacslist [['gr1 ////gr2']] $ peacnames＃library＃library（reshape2）＃＃peakNames1 < - 熔体（peakNames，value.name =“ merged.peak.id”）＃peakNames1 <-cbind（peakNames1 [，1]，do.call（rbind，strsplit，strsplit） "__"))) # colnames(peakNames1) <- c("merged.peak.id", "group", "peakName") # head(peakNames1) # gr1.subset <- gr1[peakNames1[peakNames1[, "group"] %in% "gr1", "peakName"]] # gr2.subset <- gr2[peakNames1[peakNames1[, "group"] %in% "gr2", "peakName"]] ## ----------------------------------------------------------------------------- # all.peaks <- ol$all.peaks # gr1.renamed <- all.peaks$gr1 # gr2.renamed <- all.peaks$gr2 # peakNames <- melt(ol$peaklist[['gr1///gr2']]$peakNames, value.name="merged.peak.id") # gr1.sub <- gr1.renamed[peakNames[grepl("^gr1", peakNames[, 3]), 3]] # gr2.sub <- gr2.renamed[peakNames[grepl("^gr2", peakNames[, 3]), 3]]