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).

1 | ```
combinatorialStates(hmm.list, binary = FALSE)
``` |

`hmm.list` |
A list of models generated by |

`binary` |
If |

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 |

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

Aaron Taudt

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | ```
# 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,
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)
``` |

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