PeakError: PeakError

In PeakError: Compute the Annotation Error of Peak Calls

Description

Compute true and false positive peak calls, with respect to a database of annotated regions.

Usage

PeakError(peaks, regions)

Arguments

peaks	data.frame with columns chrom, chromStart, chromEnd. NOTE: chromStart should be 0-based and chromEnd should be 1-based. EXAMPLE: the first 100 base of of a chromosome are chromStart=0, chromEnd=100. The second 100 bases are chromStart=100, chromEnd=200.
regions	data.frame with columns chrom, chromStart, chromEnd, annotation.

Value

data.frame for each region with additional counts of true positives (tp, possible.tp), false positives (fp, possible.fp, fp.status), and false negatives (fn, fn.status).

Author(s)

Toby Dylan Hocking

Examples

x <- seq(5, 85, by=5)
peaks <- rbind(Peaks("chr2", x, x+3),
               Peaks("chr3", c(25, 38, 57), c(33, 54, 75)),
               Peaks("chr4", c(5, 32, 38, 65), c(15, 35, 55, 85)),
               Peaks("chr5", c(12, 26, 56, 75), c(16, 54, 59, 85)))
regions <- NULL
for(chr in 1:5){
  regions <- rbind(regions, {
    data.frame(chrom=paste0("chr", chr),
               chromStart=c(10, 30, 50, 70),
               chromEnd=c(20, 40, 60, 80),
               annotation=c("noPeaks", "peakStart", "peakEnd", "peaks"))
  })
}
err <- PeakError(peaks, regions)
ann.colors <-
  c(noPeaks="#f6f4bf",
    peakStart="#ffafaf",
    peakEnd="#ff4c4c",
    peaks="#a445ee")
library(ggplot2)
ggplot()+
  geom_rect(aes(xmin=chromStart+1/2, xmax=chromEnd+1/2,
                ymin=-1, ymax=1,
                fill=annotation,
                linetype=fn.status,
                size=fp.status),
            data=err, color="black")+
  scale_y_continuous("", breaks=NULL)+
  scale_linetype_manual(values=c("false negative"="dotted", correct="solid"))+
  scale_size_manual(values=c("false positive"=3, correct=1))+
  scale_fill_manual(values=ann.colors, breaks=names(ann.colors))+
  facet_grid(chrom ~ .)+
  theme_bw()+
  guides(fill=guide_legend(order=1),
         linetype=guide_legend(order=2, override.aes=list(fill="white")),
         size=guide_legend(order=3, override.aes=list(fill="white")))+
  theme(panel.margin=grid::unit(0, "cm"))+
  geom_segment(aes(chromStart+1/2, 1/2, xend=chromEnd+1/2, yend=1/2),
               data=peaks, color="deepskyblue", size=2)+
  scale_x_continuous("position on chromosome",
                     breaks=seq(10, 90, by=10))+
  geom_text(aes(base, -1/2, label="N"), data.frame(base=10:90),
            color="deepskyblue")

PeakError documentation built on May 2, 2019, 8:29 a.m.