| sRNADiff-class {srnadiff} | R Documentation |
An S4 class to represent sRNA-Seq data for differential expression.
annotationThe annotation in GRanges format.
bamFileNamesThe name of one read file in BAM format.
bamFilesThe BAM files in a BamFileList.
chromosomesThe names of the chromosomes.
chromosomeSizesThe sizes of the chromosomes.
replicatesThe names of the replicates.
conditionsThe condition to which each replicate belongs.
coveragesThe coverages, a vector of RLE.
lengthsThe lengths parts of the coverages.
valuesThe values parts of the coverages.
designExperimental design, a DataFrame for
DESeq2
regionsA GenomicRanges of the possibly differentially
expressed region
minDepthMinimum depth to consider to find regions
minSizeMinimum region size
maxSizeMaximum region size
mergeDistanceDistance to merge consecutive region
minDifferencesMinimum number of different nt between two regions
noDiffToDiffTransition probability
diffToNoDiffTransition probability
emissionEmission probability
emissionThresholdEmission threshold
skipAnnotationWhether to skip the annotation strategy step
skipNaiveWhether to skip the naive strategy step
skipHmmWhether to skip the HMM strategy step
skipSliceWhether to skip the slice strategy step
nThreadsNumber of threads