Differential Expression of Small RNA-Seq

Documentation for package ‘srnadiff’ version 1.2.0

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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.