plotHistogram {chromstaR} | R Documentation |
Plot a histogram of binned read counts with fitted mixture distributions from a uniHMM
object.
plotHistogram(model, state = NULL, chromosomes = NULL, start = NULL, end = NULL, linewidth = 1)
model |
A |
state |
Plot the histogram only for the specified state. One of |
chromosomes, start, end |
Plot the histogram only for the specified chromosomes, start and end position. |
linewidth |
Width of the distribution lines. |
A ggplot
object.
## 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)