chr11first: Counts of first base of aligned reads

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

Counts of first base of aligned reads

Description

For 4 samples on chr11 (hg19), this data set counts the first base pair of aligned reads at each genomic position. In contrast, chr11ChIPseq counts every base pair in each read (and each read is about 100bp, so that means there is some auto-correlation in chr11ChIPseq, but not in chr11first).

Usage

data("chr11first")

Format

A data frame with 23252 observations on the following 4 variables.

sample.id

a factor with levels for each of 4 samples

chromStart

integer vector: base before, on chr11

chromEnd

integer vector: last base on chr11

count

integer: aligned first base read counts

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)
data(chr11first)
library(ggplot2)
ann.colors <-
  c(noPeaks="#f6f4bf",
    peakStart="#ffafaf",
    peakEnd="#ff4c4c",
    peaks="#a445ee")
both <- list(coverage=chr11ChIPseq$coverage, first=chr11first)
representations <- NULL
one.sample <- "McGill0322"
for(data.type in names(both)){
  one <- subset(both[[data.type]], sample.id==one.sample)
  representations <- rbind(representations, data.frame(data.type, one))
}
one.sample.regions <- subset(
  chr11ChIPseq$regions, sample.id==one.sample)

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=one.sample.regions, alpha=1/2)+
  theme_bw()+
  theme(panel.margin=grid::unit(0, "cm"))+
  facet_grid(data.type ~ ., scales="free")+
  geom_step(aes(chromStart/1e3, count), data=representations)+
  xlab("position on chr11 (kilo base pairs)")

}

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