sRNADiff-class {srnadiff} | R Documentation

## An S4 class to represent sRNA-Seq data for differential expression.

### Description

An S4 class to represent sRNA-Seq data for differential expression.

### Slots

`annotation`

  The annotation in GRanges format.

`bamFileNames`

  The name of one read file in BAM format.

`bamFiles`

  The BAM files in a `BamFileList`.

`chromosomes`

  The names of the chromosomes.

`chromosomeSizes`

  The sizes of the chromosomes.

`replicates`

  The names of the replicates.

`conditions`

  The condition to which each replicate belongs.

`coverages`

  The coverages, a vector of `RLE`.

`lengths`

  The lengths parts of the coverages.

`values`

  The values parts of the coverages.

`design`

  Experimental design, a `DataFrame` for `DESeq2`

`regions`

  A `GenomicRanges` of the possibly differentially expressed region

`minDepth`

  Minimum depth to consider to find regions

`minSize`

  Minimum region size

`maxSize`

  Maximum region size

`mergeDistance`

  Distance to merge consecutive region

`minDifferences`

  Minimum number of different nt between two regions

`noDiffToDiff`

  Transition probability

`diffToNoDiff`

  Transition probability

`emission`

  Emission probability

`emissionThreshold`

  Emission threshold

`skipAnnotation`

  Whether to skip the annotation strategy step

`skipNaive`

  Whether to skip the naive strategy step

`skipHmm`

  Whether to skip the HMM strategy step

`skipSlice`

  Whether to skip the slice strategy step

`nThreads`

  Number of threads

[Package srnadiff version 1.0.0 Index]