multiClusterPeaks: multiClusterPeaks

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

multiClusterPeaks

Description

Cluster peaks into overlapping groups.

Usage

multiClusterPeaks(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

library(PeakSegJoint)
data(chr7.peaks, envir=environment())
library(ggplot2)
ggplot()+
  geom_segment(aes(
    chromStart/1e3, sample.id,
    xend=chromEnd/1e3, yend=sample.id),
    data=chr7.peaks)

clustered <- multiClusterPeaks(chr7.peaks)
clustered.list <- split(clustered, clustered$cluster)
clusters.list <- list()
for(cluster.name in names(clustered.list)){
  clusters.list[[cluster.name]] <- with(
    clustered.list[[cluster.name]], data.frame(
      cluster=cluster[1],
      clusterStart=as.integer(median(chromStart)),
      clusterEnd=as.integer(median(chromEnd))))
}
clusters <- do.call(rbind, clusters.list)
ggplot()+
  geom_segment(aes(
    chromStart/1e3, sample.id,
    color=factor(cluster),
    xend=chromEnd/1e3, yend=sample.id),
    data=clustered)+
geom_segment(aes(
  clusterStart/1e3, "clusters",
  color=factor(cluster),
  xend=clusterEnd/1e3, yend="clusters"),
  data=clusters)

tdhock/PeakSegJoint documentation built on Jan. 27, 2024, 9 p.m.