Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>
Author: Toby Dylan Hocking
Version: 2023.9.4
License: GPL-3
Title: Compute the Label Error of Peak Calls
Description: Chromatin immunoprecipitation DNA sequencing results in genomic tracks that show enriched regions or peaks where proteins are bound. This package implements fast C code that computes the true and false positives with respect to a database of annotated region labels.
Suggests: testthat, ggplot2
NeedsCompilation: yes
Packaged: 2023-09-06 04:49:01 UTC; tdhock
Repository: CRAN
Date/Publication: 2023-09-06 05:20:02 UTC

PeakError

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.list <- list()
for(chr in 1:5){
  regions.list[[chr]] <- data.frame(
    chrom=paste0("chr", chr),
    chromStart=c(10, 30, 50, 70),
    chromEnd=c(20, 40, 60, 80),
    annotation=c("noPeaks", "peakStart", "peakEnd", "peaks"))
}
regions <- do.call(rbind, regions.list)
err <- PeakError(peaks, regions)
ann.colors <- c(
  noPeaks="#f6f4bf",
  peakStart="#ffafaf",
  peakEnd="#ff4c4c",
  peaks="#a445ee")
if(require(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")
}

PeakErrorChrom

Description

Compute the PeakError assuming that peaks and regions are on the same chrom.

Usage

PeakErrorChrom(peaks, 
    regions)

Arguments

peaks

data.frame with columns 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 chromStart, chromEnd.

Value

data.frame with 1 row for each region and error columns.

Author(s)

Toby Dylan Hocking

Peaks

Description

Make a data.frame that represents a list of peaks.

Usage

Peaks(chrom = factor(), 
    base.before = integer(), 
    last.base = integer())

Arguments

chrom

character or factor with chrom name for example "chr22"

base.before

integer, base before peak.

last.base

integer, last base of peak.

Value

data.frame with columns chrom, chromStart, chromEnd.

Author(s)

Toby Dylan Hocking

checkChrom

Description

Check for a valid data.frame with chrom names.

Usage

checkChrom(df)

Arguments

df

df

Author(s)

Toby Dylan Hocking

checkPositions

Description

Check for a valid data.frame with chromStart, chromEnd.

Usage

checkPositions(df)

Arguments

df

df

Author(s)

Toby Dylan Hocking