clusterPeaks: clusterPeaks

In PeakSegJoint: Joint Peak Detection in Several ChIP-Seq Samples

clusterPeaks

Description

Cluster peaks into overlapping groups.

Usage

clusterPeaks(peaks)

Arguments

peaks

data.frame with columns chromStart, chromEnd.

Value

peaks data.frame, sorted by chromStart, with an additional column cluster.

Author(s)

Toby Dylan Hocking

Examples

unordered <-
  data.frame(chromStart=c(11, 12, 1, 2, 3, 6, 7),
             chromEnd=c(13, 14, 5, 8, 4, 9, 10),
             sample.id=factor(paste0("sample.", c(1, 2, 1, 2, 3, 4, 5))))
clustered <- clusterPeaks(unordered)
library(ggplot2)
bases <- geom_text(aes(position, "base", label=base),
                   data=data.frame(position=1:20, base="N"))
gg <- ggplot()+bases+ylab("")+
  scale_x_continuous(breaks=1:20)

gg+
  geom_segment(aes(chromStart+1/2, sample.id,
                   xend=chromEnd+1/2, yend=sample.id),
                   data=clustered)+
  theme_bw()+
  theme(panel.margin=grid::unit(0, "cm"))+
  facet_grid(.~cluster, labeller=label_both, scales="free", space="free")

gg+
  geom_segment(aes(chromStart+1/2, sample.id,
                   xend=chromEnd+1/2, yend=sample.id, color=factor(cluster)),
                   data=clustered)

PeakSegJoint documentation built on April 25, 2023, 9:12 a.m.