changePostCutoff: Change the posterior cutoff of a Hidden Markov Model

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

Description

Adjusts the peak calls of a uniHMM, multiHMM or combinedMultiHMM object with the given posterior cutoff.

Usage

changePostCutoff(model, post.cutoff = 0.5)

Arguments

model	A uniHMM or multiHMM object with posteriors.
post.cutoff	A vector of posterior cutoff values between 0 and 1 the same length as ncol(model$bins$posteriors). If only one value is given, it will be reused for all columns. Values close to 1 will yield more stringent peak calls with lower false positive but higher false negative rate.

Details

Posterior probabilities are between 0 and 1. Peaks are called if the posteriors for a state (univariate) or sample (multivariate) are >= post.cutoff.

Value

The input object is returned with adjusted peak calls.

Author(s)

Aaron Taudt

See Also

changeMaxPostCutoff

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 HMM
model <- callPeaksUnivariate(binned, keep.posteriors=TRUE, verbosity=0)
## Compare fits with different post.cutoffs
plotHistogram(changePostCutoff(model, post.cutoff=0.01)) + ylim(0,0.25)
plotHistogram(model) + ylim(0,0.25)
plotHistogram(changePostCutoff(model, post.cutoff=0.99)) + ylim(0,0.25)

## Get an example multiHMM ##
file <- system.file("data","multivariate_mode-combinatorial_condition-SHR.RData",
                    package="chromstaR")
model <- get(load(file))
genomicFrequencies(model)
model.new <- changePostCutoff(model, post.cutoff=0.9999)
genomicFrequencies(model.new)

## Get an example combinedMultiHMM ##
file <- system.file("data","combined_mode-differential.RData",
                    package="chromstaR")
model <- get(load(file))
genomicFrequencies(model)
model.new <- changePostCutoff(model, post.cutoff=0.9999)
genomicFrequencies(model.new)

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