plotHistogram: Histogram of binned read counts with fitted mixture...

In chromstaR: Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

Description

Plot a histogram of binned read counts with fitted mixture distributions from a uniHMM object.

Usage

plotHistogram(
  model,
  state = NULL,
  chromosomes = NULL,
  start = NULL,
  end = NULL,
  linewidth = 1
)

Arguments

model	A uniHMM object or file that contains such an object.
state	Plot the histogram only for the specified state. One of c('unmodified','modified').
chromosomes, start, end	Plot the histogram only for the specified chromosomes, start and end position.
linewidth	Width of the distribution lines.

Value

A ggplot object.

See Also

plotting

Examples

## Get an example BAM file with ChIP-seq reads
file <- system.file("extdata", "euratrans",
                      "lv-H3K27me3-BN-male-bio2-tech1.bam",
                       package="chromstaRData")
## Bin the BED file into bin size 1000bp
data(rn4_chrominfo)
data(experiment_table)
binned <- binReads(file, experiment.table=experiment_table,
                  assembly=rn4_chrominfo, binsizes=1000,
                  stepsizes=500, chromosomes='chr12')
plotHistogram(binned)
## Fit the univariate Hidden Markov Model
hmm <- callPeaksUnivariate(binned, max.time=60, eps=1)
## Check if the fit is ok
plotHistogram(hmm)

chromstaR documentation built on Nov. 8, 2020, 8:29 p.m.