Refactored basic 6-state hmm. New classes HmmParam, EmissionParam,... Addition of several unit tests
Added a bunch of unit tests, as well as classes based on SummarizedExperiment
several refactorings
several refactorings
update unit tests
Fix unit test
Removed Biobase from imports
Removed several packages from imports. Moved GenomicRanges to Depends
Add classes for GRanges with HMM states (HmmGRanges) and a SummarizedHMM class (necessary?) for storing the HmmGRanges and the forward/backward variables
Add methods-HmmGRanges and methods-SummarizedHMM
bump to v1.25.10
more refactoring
resolve conflict in merging of SummarizedExperiment branch with master
calculateTransitionProb method for oligoSnpSet. Add chromosome slot to HmmParam object
HMM is fit to all chromosomes simultaneously.
version passes unit tests
update man files for VI using roxygen
added new Rd files
bumped version: 1.27.6
fixed 'Error in get_tags' from document() by providing additional documention to a constructor for a class (title, description, param)

#' SnpArrayExperiment container for log R ratios and B allele frequencies
#'
#' Constructor for SnpArrayExperiment
#'
#' @param cn matrix of copy number estimates (e.g., log R ratios)
#' @param baf  matrix of B allele frequencies
#' @param rowData GRanges object for SNPs/nonpolymorphic markers
#' @param colData DataFrame containing sample-level covariates
#' @param isSnp  logical vector indicating whether marker is a SNP