PeakSegJointError: PeakSegJointError

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

PeakSegJointError

Description

Compute number of incorrect regions for every PeakSegJoint model.

Usage

PeakSegJointError(converted, 
    problem.regions)

Arguments

converted	Result of ConvertModelList.
problem.regions	data.frame of annotated region labels.

Value

List of error.totals (data.frame with one row for each model size, with counts of incorrect labels), error.regions (list of data.frames with labels and error status for each model size), modelSelection (data.frame with one row for each model from exactModelSelection), target (numeric vector of length 2, lower and upper limits of target interval of log.lambda penalty values in the interval regression problem).

Author(s)

Toby Dylan Hocking

Examples

library(PeakSegJoint)
data(H3K36me3.TDH.other.chunk1, envir=environment())
lims <- c(43000000, 43200000) # left
some.counts <-
  subset(H3K36me3.TDH.other.chunk1$counts,
         lims[1] < chromEnd & chromStart < lims[2])
some.regions <-
  subset(H3K36me3.TDH.other.chunk1$regions,
         lims[1] < chromEnd & chromStart < lims[2])
fit <- PeakSegJointSeveral(some.counts)
converted <- ConvertModelList(fit)
error.list <- PeakSegJointError(converted, some.regions)

peaks.int.vec <- 1:3
show.peaks <- subset(converted$peaks, peaks %in% peaks.int.vec)
show.labels <- do.call(rbind, error.list$error.regions[paste(peaks.int.vec)])

if(interactive() && require(ggplot2)){
  ann.colors <-
    c(noPeaks="#f6f4bf",
      peakStart="#ffafaf",
      peakEnd="#ff4c4c",
      peaks="#a445ee")
  ggplot()+
    penaltyLearning::geom_tallrect(aes(
      xmin=chromStart/1e3, xmax=chromEnd/1e3, fill=annotation),
      alpha=0.5,
      color="grey",
      data=some.regions)+
    scale_fill_manual(values=ann.colors)+
    scale_linetype_manual("error type",
                          limits=c("correct", 
                                   "false negative",
                                   "false positive"
                                   ),
                          values=c(correct=0,
                                   "false negative"=3,
                                   "false positive"=1))+
    geom_step(aes(chromStart/1e3, count),
              color="grey50",
              data=some.counts)+
    penaltyLearning::geom_tallrect(aes(
      xmin=chromStart/1e3, xmax=chromEnd/1e3, linetype=status),
      fill=NA,
      color="black",
      size=1,
      data=show.labels)+
    geom_segment(aes(chromStart/1e3, 0,
                     xend=chromEnd/1e3, yend=0),
                 size=3,
                 color="deepskyblue",
                 data=show.peaks)+
    theme_bw()+
    theme(panel.margin=grid::unit(0, "cm"))+
    facet_grid(sample.id ~ peaks, scales="free")
}

PeakSegJoint documentation built on April 25, 2023, 9:12 a.m.