combinatorialStates: Get the (decimal) combinatorial states of a list of...

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

Description

Get the combinatorial states of a list of models generated by callPeaksUnivariate. The function returns the decimal combinatorial states for each bin (see details for an explanation of combinatorial state).

Usage

combinatorialStates(hmm.list, binary = FALSE)

Arguments

hmm.list	A list of models generated by callPeaksUnivariate, e.g. 'list(model1,model2,...)'.
binary	If TRUE, a matrix of binary instead of decimal states will be returned.

Details

For a given model, each genomic bin can be either called 'unmodified' or 'modified', depending on the posterior probabilities estimated by the Baum-Welch. Thus, a list of models defines a binary combinatorial state for each bin. This binary combinatorial state can be expressed as a decimal number. Example: We have 4 histone modifications, and we run the univariate HMM for each of them. Then we use a false discovery rate of 0.5 to call each bin either 'unmodified' or 'modified'. The resulting binary combinatorial states can then be converted to decimal representation. The following table illustrates this:

bin	modification state				decimal state
	model1	model2	model3	model4
1	0	0	1	0	2
2	0	0	0	0	0
3	0	1	1	0	6
4	0	1	1	1	7

Value

Output is a vector of integers representing the combinatorial state of each bin.

Author(s)

Aaron Taudt

See Also

dec2bin, bin2dec

Examples

# Get example BAM files for 3 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(1,4,6)]
# 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)
}
## Get the decimal representation of the combinatorial state of this combination of models
states <- chromstaR:::combinatorialStates(models, binary=FALSE)
## Show number of each state
table(states)

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