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. |