chr11ChIPseq: ChIP-seq aligned read coverage for 4 samples on a subset of...

In PeakSegDP: Dynamic Programming Algorithm for Peak Detection in ChIP-Seq Data

ChIP-seq aligned read coverage for 4 samples on a subset of chr11

Description

A ChIP-seq experiment was performed to locate the genomic positions of a histone (H3K4me3) in 2 B cell samples (McGill0091, McGill0322) and 2 T cell samples (McGill0002, McGill0004). The short sequence reads (about 100 base pairs each) were aligned to the hg19 reference genome, and the "coverage" in this data set contains the total count of aligned reads at each base pair. It also contains annotated regions determined by an expert who examined scatterplots of the coverage profiles.

Usage

data("chr11ChIPseq")

Format

A named list of 2 data.frames: regions contains annotations about which regions contain or do not contain peaks, and coverage contains the noisy signal.

Source

H3K4me3_TDH_immune chunk 5 in http://cbio.ensmp.fr/~thocking/chip-seq-chunk-db/ which in turn comes from http://epigenomesportal.ca/

Examples

data(chr11ChIPseq)
library(ggplot2)
ann.colors <-
  c(noPeaks="#f6f4bf",
    peakStart="#ffafaf",
    peakEnd="#ff4c4c",
    peaks="#a445ee")

if(interactive() && require(ggplot2)){

ggplot()+
  scale_fill_manual("annotation", values=ann.colors,
                    breaks=names(ann.colors))+
  penaltyLearning::geom_tallrect(aes(xmin=chromStart/1e3, xmax=chromEnd/1e3,
                    fill=annotation),
                data=chr11ChIPseq$regions, alpha=1/2)+
  theme_bw()+
  theme(panel.margin=grid::unit(0, "cm"))+
  facet_grid(sample.id ~ ., scales="free")+
  geom_step(aes(chromStart/1e3, count), data=chr11ChIPseq$coverage)+
  xlab("position on chr11 (kilo base pairs)")

}

PeakSegDP documentation built on May 29, 2024, 3:45 a.m.