Differential Expression of Small RNA-Seq


[Up] [Top]

Documentation for package ‘srnadiff’ version 1.0.0

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.