# Differential Expression of Small RNA-Seq

## Documentation for package ‘srnadiff’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

srnadiff-package | srnadiff: A package for differential expression of sRNA-Seq.
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
regions-method | 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.
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).
setEmissionProbabilities-method | 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.
setEmissionThreshold-method | 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)
setMergeDistance-method | Set the threshold to merge close regions (in the naive step)
setMinDepth | Set min minimum depth to localize regions
setMinDepth-method | Set min minimum depth to localize regions
setMinDifferences | Set the threshold to remove similar regions (in the slice step)
setMinDifferences-method | 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.
setMinOverlap-method | 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
setNThreads-method | Set number of threads to use
setSizes | Set min and max sizes of the regions
setSizes-method | Set min and max sizes of the regions
setStrategies | Set the different steps
setStrategies-method | Set the different steps
setTransitionProbabilities | Set transition probabilities (for the HMM step).
setTransitionProbabilities-method | Set transition probabilities (for the HMM step).
show-method | Overloading the show method
srnadiff | srnadiff: A package for differential expression of sRNA-Seq.
sRNADiff-class | An S4 class to represent sRNA-Seq data for differential expression.
sRNADiffExample | Example constructor
sRNADiffExp | Constructor.