Man pages for mzytnicki/srnadiff
Differential Expression of Small RNA-Seq

buildDataHmmRead the coverage and extract expressed regions
computePvaluesCompute p-values of the selected counts.
plotRegionPlot a region
rcpp_buildHmmCompute unique counts.
rcpp_naiveCompute naive method.
rcpp_normalizationNormalize counts (and changes the input values)
rcpp_sliceCompute unique counts.
rcpp_viterbiRun the Viterbi algorithm on the HMM.
readAnnotationSegmentation using an annotation file.
readMiRBaseMatureAnnotationSegmentation using an miRBase annotation file and use mature...
readMiRBasePreAnnotationSegmentation using an miRBase annotation file and use...
readWholeGenomeAnnotationSegmentation using an annotation file that contains every...
regions-methodGet the output regions
runAllRun the segmentation using 3 different methods, and...
runAllAnnotationSegmentation using an annotation file.
runAllHmmSegmentation of the genome using an HMM.
runAllNaiveSegmentation of the genome in a naive way.
runAllSliceSegmentation of the genome using a slice method.
runHmmInitialize and run the HMM.
runSliceInitialize and run the slice method.
setEmissionProbabilities-methodSet emission probabilities (for the HMM step): probability to...
setEmissionThreshold-methodSet emission threshold (for the HMM step): the emission...
setMergeDistance-methodSet the threshold to merge close regions (in the naive step)
setMinDepth-methodSet min minimum depth to localize regions
setMinDifferences-methodSet the threshold to remove similar regions (in the slice...
setMinOverlap-methodSet minimum overlap (for the last quantification step): all...
setNThreads-methodSet number of threads to use
setSizes-methodSet min and max sizes of the regions
setStrategies-methodSet the different steps
setTransitionProbabilities-methodSet transition probabilities (for the HMM step).
show-sRNADiff-methodOverloading the show method
srnadiffsrnadiff: A package for differential expression of sRNA-Seq.
sRNADiff-classAn S4 class to represent sRNA-Seq data for differential...
sRNADiffExampleExample constructor
mzytnicki/srnadiff documentation built on Feb. 3, 2018, 11:01 p.m.