unis2pseudomulti: Combine univariate HMMs to a multivariate HMM

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

Description

Combine multiple uniHMMs to a multiHMM without running callPeaksMultivariate. This should only be done for comparison purposes.

Usage

unis2pseudomulti(hmms)

Arguments

hmms	A named list of uniHMM objects. Names will be used to generate the combinations.

Details

Use this function if you want to combine ChIP-seq samples without actually running a multivariate Hidden Markov Model. The resulting object will be of class multiHMM but will not be truly multivariate.

Value

A multiHMM object.

Author(s)

Aaron Taudt

Examples

# Get example BAM files for 2 different marks in hypertensive rat (SHR)
file.path <- system.file("extdata","euratrans", package='chromstaRData')
files <- list.files(file.path, full.names=TRUE, pattern='SHR.*bam$')[c(1,4)]
# Bin the data
data(rn4_chrominfo)
binned.data <- list()
for (file in files) {
 binned.data[[basename(file)]] <- binReads(file, binsizes=1000, stepsizes=500,
                                           assembly=rn4_chrominfo, chromosomes='chr12')
}
# Obtain the univariate fits
models <- list()
for (i1 in 1:length(binned.data)) {
 models[[i1]] <- callPeaksUnivariate(binned.data[[i1]], max.time=60, eps=1)
}
## Combine the univariate HMMs without fitting a multivariate HMM
names(models) <- c('H3K27me3','H3K4me3')
pseudo.multi.HMM <- unis2pseudomulti(models)
## Compare frequencies with real multivariate HMM
exp <- data.frame(file=files, mark=c("H3K27me3","H3K4me3"),
                 condition=rep("SHR",2), replicate=c(1,1), pairedEndReads=FALSE,
                 controlFiles=NA)
states <- stateBrewer(exp, mode='combinatorial')
real.multi.HMM <- callPeaksMultivariate(models, use.states=states, eps=1, max.time=60)
genomicFrequencies(real.multi.HMM)
genomicFrequencies(pseudo.multi.HMM)

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