sRNADiff-class {srnadiff} | R Documentation |
An S4 class to represent sRNA-Seq data for differential expression.
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