PeakSegJointError function

PeakSegJointError

Compute number of incorrect regions for every PeakSegJoint model.

PeakSegJointError(converted, 
    problem.regions)

Arguments

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

Returns

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 toby.hocking@r-project.org [aut, cre]

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")
}