mixZIHMMConstr: Three-state HMM with mixture model for differential peak...

In plbaldoni/mixHMM: Differential Peak Calling via Hidden Markov Model With Mixture of Negative Binomial Distributions

Description

This function fits a three-state HMM with mixture model of Zero-Inflated Negative Binomials (ZINB) and Negative Binomials (NB) for differential peaks across conditions with replicates. The emission distribution of the HMM component associated with background counts follows a ZINB distribution. The emission distribution of the HMM component associated with enrichment counts in consensus follows a NB distribution. Only five parameters are associated with the emission distributions of this three-state HMM: zero-inflation probability, mean and dispersion of background counts, and mean and dispersion of enrichment counts.

Usage

mixZIHMMConstr(ChIP, Control = NULL, offset, group, control)

Arguments

ChIP	M*N matrix of ChIP read counts, where M is the number of windows in the analyzed genome and N is the number of conditions*replicates.
Control	M*N matrix of log-transformed Control read counts (not yet implemented)
offset	M*N matrix of offsets. If no offset is used, use offset = matrix(0,nrow=M,ncol=N)
group	vector of length N with condition (numeric) labels (e.g. c(1,1,2,2,3,3) for three conditions and two replicates each)
control	list of control arguments from controlPeaks()

Details

For ChIP, Control, and offset matrices, columns should be ordered by condition and replicates, respectively. For instance, the first column should have data from the first replicate of the first condition, the second column should have data from the second replicate of the first condition, and so on. The same applies for the elements of group.

Value

A list with components

Author(s)

Pedro L. Baldoni, [e-mail]

References

https://github.com/plbaldoni/mixHMM

Examples

data(H3K36me3)
ChIP = SummarizedExperiment::assay(H3K36me3)
offset = ZIMHMM::createOffset(ChIP,method = 'ratio')
group = c(1,1,1,2,2,2,3,3,3)
B = 2^(length(unique(group)))-2
## Not run: output = mixZIHMMConstr(ChIP,Control=NULL,offset,group,B,control = controlPeaks())

plbaldoni/mixHMM documentation built on Nov. 8, 2019, 8:05 p.m.