buildDataHmm            Read the coverage and extract expressed regions
computePvalues          Compute p-values of the selected counts.
plotRegion              Plot a region
rcpp_buildHmm           Compute unique counts.
rcpp_naive              Compute naive method.
rcpp_normalization      Normalize counts (and changes the input values)
rcpp_slice              Compute unique counts.
rcpp_viterbi            Run the Viterbi algorithm on the HMM.
readAnnotation          Segmentation using an annotation file.
readMiRBaseMatureAnnotation
                        Segmentation using an miRBase annotation file
                        and use mature miRNAs.
readMiRBasePreAnnotation
                        Segmentation using an miRBase annotation file
                        and use precursor miRNAs.
readWholeGenomeAnnotation
                        Segmentation using an annotation file that
                        contains every genomic feature; it extracts the
                        miRNAs.
regions                 Get the output regions
runAll                  Run the segmentation using 3 different methods,
                        and reconciliate them.
runAllAnnotation        Segmentation using an annotation file.
runAllHmm               Segmentation of the genome using an HMM.
runAllNaive             Segmentation of the genome in a naive way.
runAllSlice             Segmentation of the genome using a slice
                        method.
runHmm                  Initialize and run the HMM.
runSlice                Initialize and run the slice method.
sRNADiff-class          An S4 class to represent sRNA-Seq data for
                        differential expression.
sRNADiffExample         Example constructor
sRNADiffExp             Constructor.
setEmissionProbabilities
                        Set emission probabilities (for the HMM step):
                        probability to have a p-value not less than a
                        threshold in the "not-differentially expressed"
                        state, and a p-value not greater than this
                        threshold in the "differentially expressed"
                        state (supposed equal).
setEmissionThreshold    Set emission threshold (for the HMM step): the
                        emission distribution being binomial, all the
                        p-values less than this threshold belong to one
                        class, and all the p-values greater than this
                        threshold belong to the other class.
setMergeDistance        Set the threshold to merge close regions (in
                        the naive step)
setMinDepth             Set min minimum depth to localize regions
setMinDifferences       Set the threshold to remove similar regions (in
                        the slice step)
setMinOverlap           Set minimum overlap (for the last
                        quantification step): all the reads with at
                        least n nucleotides shared with a feature will
                        be used for quantification of this feature.
setNThreads             Set number of threads to use
setSizes                Set min and max sizes of the regions
setStrategies           Set the different steps
setTransitionProbabilities
                        Set transition probabilities (for the HMM
                        step).
show,sRNADiff-method    Overloading the show method
srnadiff                srnadiff: A package for differential expression
                        of sRNA-Seq.
