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## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE, eval = FALSE,
warning = FALSE, error = FALSE)
## -----------------------------------------------------------------------------
# p1 <- GRanges("1", IRanges(c(1, 4, 7), width=2))
# p2 <- GRanges("1", IRanges(c(2, 5), width=3))
# ol_min <- findOverlapsOfPeaks(p1, p2, connectedPeaks="min")
# ## the counts will be the minimal peaks involved in that group of
# ## connected peaks, so you get 2.
# ol_merge <- findOverlapsOfPeaks(p1, p2, connectedPeaks="merge")
# ## the counts will be 1 for each group of connected peaks
# ol_min$venn_cnt
# ol_merge$venn_cnt
## -----------------------------------------------------------------------------
# library(ChIPpeakAnno)
# bed <- system.file("extdata", "MACS_output.bed", package="ChIPpeakAnno")
# gr1 <- toGRanges(bed, format="BED", header=FALSE)
# gff <- system.file("extdata", "GFF_peaks.gff", package="ChIPpeakAnno")
# gr2 <- toGRanges(gff, format="GFF", header=FALSE, skip=3)
# ol <- findOverlapsOfPeaks(gr1, gr2)
# peakNames <- ol$peaklist[['gr1///gr2']]$peakNames
# library(reshape2)
# peakNames1 <- melt(peakNames, value.name="merged.peak.id")
# peakNames1 <- cbind(peakNames1[, 1], do.call(rbind, strsplit(as.character(peakNames1[, 3]), "__")))
# colnames(peakNames1) <- c("merged.peak.id", "group", "peakName")
# head(peakNames1)
# gr1.subset <- gr1[peakNames1[peakNames1[, "group"] %in% "gr1", "peakName"]]
# gr2.subset <- gr2[peakNames1[peakNames1[, "group"] %in% "gr2", "peakName"]]
## -----------------------------------------------------------------------------
# all.peaks <- ol$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]]
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